2.2.1 Water temperature monitoring

Depending on the spatial distribution of local effects (e.g., due to a point discharge, reservoir, etc.) or more widely across a watershed scale, several temperature monitoring techniques may be employed. Digital temperature data loggers (thermographs) are among the most widespread instruments in use for continuous monitoring of water temperatures in aquatic ecosystems. Thermographs are generally mounted securely in a representative location (e.g., pool, riffle, etc.) for one or more seasons, and data are regularly downloaded. A number of considerations in deploying and collecting temperature data are important, including number of times temperature is monitored, interval of collection, and location of sites (Dunham et al. 2005).

In addition to direct temperature monitoring, recent remote sensing techniques such as forward looking infrared radiometry (FLIR) allow for the collection of spatially continuous surface temperature profiles over large areas at one time (i.e. synoptic sampling). This could be used both as a diagnostic tool to compare affected areas with reference areas, locate particular stream reaches with temperature in excess of established criteria or discontinuities due to dams, cooling water discharges, hyporheic exchanges, or hot springs. This information could be used to further develop a continuous monitoring program to characterize and ameliorate any identified impacts. This method has been applied throughout the United States including at the Lake Chelan Hydroelectric Project (FERC Project No. 637) on the Chelan River, Washington; within the Yadkin Pee-Dee River Hydroelectric Project (FERC Project No. 2206) study area, North Carolina; and at the Norway and Oakdale Hydroelectric Project (FERC Project Nos. UL00-2, UL00-1) in the Tippecanoe River basin, Indiana.

2.2.1.1 Selected references

Dunham, J., G. Chandler, B. Rieman, and D. Martin. 2005. Measuring stream temperature with digital data loggers: a user’s guide. General Technical Report RMRSGTR-150WWW. U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station, Fort Collins, Colorado.

Torgersen, C. E., R. N. Faux, B. A. McIntosh, N. J. Poage, and D. J. Norton. 2001. Airborne thermal remote sensing for water temperature assessment in rivers and streams. Remote Sensing of Environment 76: 386-398.

2.2.2 Water temperature modeling

Information gathered during water temperature monitoring can be used to model temperature effects of dams, and to develop strategies to ameliorate temperature impacts related to project operations. Stream temperature modeling can be accomplished on both reach and basin scales. The particular choice of modeling scale is most often determined by the question at hand which, for example, could range from temperature effects related to road crossings to basin-wide issues such as forest management practices.

Reach-scale models are often used to examine localized phenomena such as alterations in the riparian canopy (e.g., roads, power lines, etc.) or cold and warm water discharges. Commonly used physical models include SSTEMP (Bartholow 2002), HeatSource (Boyd and Kasper 2003), and others that were developed from channel and valley geometry, shade estimates, hydrology, and meteorology (Brown 1969). Although they may be calibrated accurately to a known temperature record, reach-based models are sometimes unable to adequately account for large changes in model inputs outside of the validated calibration ranges, or account for other effects such as tributary mixing and hyporheic exchanges.

Basin-scale models are more often used to examine land use effects on temperature regimes, but may be applied to evaluate effects of distributed project features on downstream temperatures. Common network-based models, including SNTEMP (Theurer et al. 1984), HSPF (Bicknell et al. 1997), QUAL2k (Chapra et al 2005), and others evaluate entire watersheds by calculating the temperature of individual reaches and then hydraulically routing the heat downstream. Because network-based models require substantial field-measured input data to operate and frequently do not explicitly evaluate uncertainty, more sophisticated landscape Geographic Information System (GIS)-based models such as BasinTemp (Allen et al. 2005) have been employed over larger watersheds where temperature data may be sparse.

Water temperature modeling approaches have been applied at numerous hydroelectric facilities throughout the United States including at the Cooper Lake Hydroelectric Project (FERC Project No. 2170) on Cooper Creek, Alaska; Box Canyon Hydroelectric Project (FERC Project No. 2042) on the Box Canyon Reservoir, Washington; and at the Lake Chelan Hydroelectric Project (FERC Project No. 637) on the Chelan River, Washington.

2.2.2.1 Selected references

Allen, D., W. Dietrich, P. Baker, F. Ligon, and B. Orr. 2005. Development of a mechanistically based, basin-scale stream temperature model: applications to cumulative effects modeling. Technical Report PSW-GTR-194. USDA Forest Service.

Bartholow, J. M. 2000. The stream segment and stream network temperature models: a self-study course. Version 2.0. USGS Open File Report 99-112. U. S. Geological Survey, Fort Collins, Colorado.

Bicknell, B. R., J. C. Imhoff, J. L. Kittle, Jr. A. S. Donigian, and R. C. Johanson. 1997. Hydrological Simulation Program, FORTRAN: User's manual for Version 11. Report EPA/600/R-97/080. U. S. Environmental Protection Agency, National Exposure Research Laboratory.

Boyd, M., and B. Kasper. 2003. Analytical methods for dynamic open channel heat and mass transfer: methodology for heat source model. Version 7.0. Watershed Sciences, Portland, Oregon.

Brown, G. W. 1969. Predicting temperatures of small streams. Water Resources Research 5: 68-75.

Chapra, S. C., G. J. Pelletier, and H. Tao. 2005. QUAL2K: a modeling framework for simulating river and stream water quality. Version 2.02: documentation and users manual. Civil and Environmental Engineering Department, Tufts University, Medford, Maryland.

Sinokrot, B. A., and H. G. Stefan. 1993. Stream temperature dynamics: measurements and modeling. Water Resources Research 29: 2299-2312.

Theurer, F. D., K. A. Voos, and W. J. Miller. 1984. Instream water temperature model. Instream Flow Information Paper No. 16, FWS/OBS-84/15. U. S. Fish and Wildlife Service, Western Energy and Land Use Team, Washington, D. C.

Additional information on water temperature modeling >>

2.3.1 Lake and reservoir water sampling

Vertical water samples from lakes and reservoirs can be used to determine the characteristic structures of lakes in summer and winter and to determine important transition periods such as fall overturn, when bottom waters are rapidly exchanged with surface waters. To represent reservoir water quality and structure, in-situ profiles of physical water quality (e.g., temperature, dissolved oxygen [DO], conductivity, pH, turbidity) are collected from the reservoir surface to near the bottom of the deeper portions of each reservoir using available multiple parameter instruments (e.g., HydroLab, YSI). Depending on the resulting temperature and dissolved oxygen profiles and the current and past land uses in the basin, more intensive grab sampling and analytical monitoring of nutrients and toxic substances may also be conducted.

This method has been applied at numerous facilities including at the Niagara Power Project (FERC Project No. 2216) in Lewiston Reservoir, New York; at the Packwood Lake Hydroelectric Project (FERC Project No. 2244) in Packwood Lake, Washington; and at the Klamath Hydroelectric Project (FERC Project No. 2082) in the J. C. Boyle Reservoir, Oregon.

2.3.1.1 Selected references

Horne, A. J. and C. R. Goldman 1994. Limnology. McGraw-Hill. New York.

NRCS (Natural Resources Conservation Service). 1997. National handbook of water quality monitoring. National Water and Climate Center, Portland, Oregon. 450-vi-NHWQM.

Wetzel, R.G., and Likens, G.E. 2000. Limnological analyses. Third edition. Springer, New York.

2.3.2 Reservoir sediment sampling and bioindicator monitoring

While hydroelectric project operation and maintenance is generally not associated with the discharge of sediment-bound contaminants, changes in the water column mixing discussed above coupled with the high sediment trapping efficiency of reservoirs can lead to increased concentrations of many toxic substances. Synthetic organic chemicals containing chlorine, including carbon tetrachloride and trichloroethylene, were available commercially by 1925, and the insecticidal properties of these compounds (e.g., dichloro-diphenyl-trichloroethane [DDT]) were recognized around 1940. Because of their persistence in the environment, the legacy of these and more recently developed compounds must be considered in any sampling program.

Depending on past and present land uses in both reservoirs and upstream areas, transported and deposited sediments act as sinks for contaminants in the reservoirs due to their high adsorption capacity, and in agricultural and industrial areas, may contain excess nutrients, bacteria, oil and grease, heavy metals, herbicides, pesticides, polychlorinated biphenyls (PCBs), and other materials.

If water quality samples identify analytical parameters above applicable water quality criteria or there is a known past or present activity in the watershed that may contribute to sediment contamination, a number of sediment sampling techniques are available to determine the extent and potential sources of the impairment. Because some toxic inorganic substances and organic contaminants associated with the sediments can also be bioconcentrated by the aquatic organisms present in reservoirs, site-specific bioindicators are often used to detect the presence of materials that may not be identified above the detection limits of most analytical water or sediment quality techniques. For example, fish tissue analysis is commonly used to detect the presence of mercury, arsenic, PCBs, and other contaminants. This method has been applied in several reservoirs in New England as part of Maine Department of Environmental Protection's Surface Water Ambient Toxic Monitoring Program; in the Clinch River and Watts Bar Reservoir, Tennessee; and at the Pueblo Reservoir, Colorado.

2.3.2.1 Selected references

Barbour, M. T., J. Gerritsen, B. D. Snyder, and J.B. Stribling. 1999. Rapid bioassessment protocols for use in streams and wadeable rivers: periphyton, benthic macroinvertebrates, and fish. Second edition. EPA 841-B-99-002. U. S. Environmental Protection Agency, Office of Water, Washington, D. C.

EPA (U. S. Environmental Protection Agency). 2000. Guidance for assessing chemical contaminant data for use in fish advisories. Volume 1: Fish sampling and analysis. Third edition. Office of Water, Washington, D. C. EPA 823-B-00-007.

EPA (U. S. Environmental Protection Agency). 2002. A guidance manual to support the assessment of contaminated sediments in freshwater ecosystems. Volume 3. Washington D. C. EPA-905-B02-001-C.

Hilsenhoff, W. L. 1988. Rapid field assessment of organic pollution with a family-level biotic index. Journal of the North American Benthological Society 7: 65-68.

NRCS (Natural Resources Conservation Service). 1997. National handbook of water quality monitoring. National Water and Climate Center, Portland, Oregon. 450-vi-NHWQM.

Slotton, D. G., J. E. Reuter, and C. R. Goldman. 1995. Mercury uptake patterns of biota in a seasonally anoxic northern California reservoir. Water, Air, and Soil Pollution, 80: 841-850.

Smith, A. G. 1991. Chlorinated hydrocarbon insecticides. Pages 731-916 in W. J. Hayes, Jr. and E. R. Laws Jr., editors. Handbook of pesticide toxicology. Academic Press, San Diego, California.

USACE (U.S. Army Corps of Engineers). 1997. Hydrologic engineering requirements for reservoirs. Washington, D. C. EM 1110-2-1420, CECW-EH-Y.

2.4.1 Water clarity, nutrients, and algal biomass

To assess the relative productivity of hydroelectric project reservoirs as compared with pristine sites, one commonly used tool is the trophic state index (TSI). TSI values are based on the relationship between nutrients (as measured by total phosphorus), algal biomass (chlorophyll-a), and water clarity (Secchi disk depths). A regular reservoir sampling program (e.g., quarterly, monthly) may be used to develop background data to determine the TSI. In addition to direct reporting of the TSI, comparisons to regional and national reference values may be developed to assess the severity of any identified impairment of water quality.

This method has been applied in numerous reservoirs including those within the Roanoke River Basin as part of the Roanoke River Basinwide Water Quality Management Plan, North Carolina and Virginia; at the Flaming Gorge Reservoir, Utah; and at Webbers Falls Reservoir, Oklahoma.

2.4.1.1 Selected reference

Carlson, R. E. 1977. A trophic state index for lakes. Limnology and Oceanography. 22(2): 36-369.

2.4.2 Stable isotope analysis: N15 and C13

Stable isotope analysis has increasingly been used to determine trophic relationships in aquatic food webs. In addition to assessing natural or anthropogenic sources of nutrients associated with reservoir eutrophication, stable isotopes can be used to identify subtler food web effects related to the natural flow of nutrients from headwater reaches downstream. For example, in river systems that historically or currently support salmonid populations, the amount of nitrogen arriving in the form of post-spawning carcasses has been hypothesized as a major source of natural productivity to headwater reaches. Because dams often impede or block fish migration routes, stable nitrogen isotope ratios may be used to indicate the relative contribution of food web nitrogen in biota arriving from atmospheric, biotic, or industrial sources. This analysis has also been used to document the historical distribution of anadromous fish, as described in Section 4.0.

2.4.2.1 Selected references

Finlay, J. C., S. Khandwala, and M. E. Power. 2002. Spatial scales of carbon flow in a river food web. Ecology 83:1845-1859.

Gende, S. M., R. T. Edwards, M. F. Willson, and M. S. Wipfli. 2002. Pacific salmon in aquatic and terrestrial ecosystems. BioScience 52: 917-928.

Hobson, K. A. 1999. Tracing origins and migration of wildlife using stable isotopes: a review. Oecologia 120:314-326.

McCutchan, J., W. Lewis, C. Kendall, and C. McGrath. 2003. Variation in trophic shift for stable isotope ratios of carbon, nitrogen, and sulfur. Oikos 102: 378-390.

Post, D. M. 2002. Using stable isotopes to estimate trophic position: models, methods, and assumptions. Ecology 83: 703-718.

Vander Zanden, M. J., and J. B. Rasmussen. 1999. Primary consumer d13C and d15N and the trophic position of aquatic consumers. Ecology 80: 1395-1401.

Vander Zanden, M. J., and J. B. Rasmussen. 2001. Variation in d15N and d13C trophic fractionation: implications for aquatic food web studies. Limnology and Oceanography 46: 2061-2066.

3.1.1 Hydrologic statistics

Statistical analyses of discharge records provide metrics for characterizing and assessing changes in flow regimes on an hourly, daily, monthly, and annual basis (e.g., Indicators of hydrologic alteration by Richter et al. [1996], and Range of variability approach by Richter et al. [1997, 1998]). Relevant statistical parameters for related studies vary with study objectives. An aquatic habitat study, for example, may emphasize components of the hydrograph critical to the species being studied (as discussed in Section 4.1.8); while a sediment transport study may focus on annual flow duration curves and flood frequency. Statistical analyses of project-induced changes in hydrology typically include:

• exceedance probability,
• flow duration analysis for the period of record and by water year type,
• flow duration analysis by month, season, or other biologically important period,
• mean monthly discharge (period of record and by water year type),
• analysis of 1-, 3-, and 7-day average maximum and minimum flows,
• magnitudes of annual maximum and minimum flows, and
• annual peak series analyses.

An assessment of project-induced changes in hydrology using pre- and post-project flow data should be made from gages with the longest possible period of record.

3.1.1.1 Selected references

Richter, B. D., J. V. Baumgartner, J. Powell, and D. P. Braun. 1996. A method for assessing hydrologic alteration within ecosystems. Conservation Biology 10: 1163-1174.

Richter, B. D., J. V. Baumgartner, R. Wigington, and D. P. Braun. 1997. How much water does a river need? Freshwater Biology 37: 231-249.

Richter, B. D., J. V. Baumgartner, and J. Powell. 1998. A spatial assessment of hydrologic alteration within a river network. Regulated Rivers: Research and Management 14: 329-340.

3.1.2 Classification of water year types

Dividing the hydrologic record for streams into water year types allows for characterization of important flow parameters during wet, normal, and dry periods. Characterizing the flow regime during different climate cycles can have significant ramifications for aquatic and terrestrial biological evaluations as well as for assessing sediment supply and transport during flood and drought periods. The timing (in addition to volume) of hydrologic events can also have important biological implications. For example, a summer drought may have a greater or lesser impact on aquatic species depending on whether it was preceded by a wet or dry spring.

Schemes for classifying water year type typically utilize one of three approaches:

1. analysis of annual runoff volumes from local United States Geological Survey (USGS) gage records for unregulated periods of record;
2. regional classification developed by local or state agencies to forecast annual water supply; or
3. site-specific classification developed by hydroelectric facilities to forecast and optimize their annual water supply.

The latter two approaches designed for forecasting annual water budgets are typically derived from snow pack measurements and/orUSGS flow records, and the suitability of these approaches for hydro relicensing studies are case specific.

Because the computational methods for determining the water year classification scheme in these latter two approaches varies by region, agency, and/or hydro facility and may be pre-determined prior to the onset of hydrorelicensing studies, these methods are not covered in detail here.

When utilizing unregulated USGS gage records to develop a water year classification scheme, annual runoff volumes are typically classified into either a 3-tier scheme (i.e., wet, normal, anddry) or a 5-tier scheme (i.e. wet, above normal, normal, below normal, and dry). One approachfor determining the statistical break points for a 3-tier classification system is to utilize the mean and standard deviation of the annual runoff volumes for the period of record. Under this approach, normal water years are defined as those years in which the annual runoff volume is within one standard deviation of the mean annual runoff volume for the period of record, wet water years are defined as those years in which the annual runoff volume is greater than or equal to one standard deviation above the mean annual runoff volume for the period of record, and dry water years are defined as those years in which the annual runoff volume is less than or equal to one standard deviation below the mean. Another approach to determining the statistical breakpoints for a water year classification system is to rank the annual runoff volumes and divide the data into equally sized classes, such that in a 3-tier system each class contains 33.3% of the records, and in a 5-tier system each class contains 20% of the annual runoff records.

3.1.3 Spill history

Characterizing the frequency, magnitude, and duration of reservoir spills for a project facility is often necessary to assess the biological effects of spillgate operation and the rapid change in discharge downstream of a dam during spills. Four primary sources of information may be used to develop spill histories:

1. reservoir elevation and spillgate opening records (often collected through a remote telemetric system),
2. project power generation records,
3. USGS discharge records for gages located directly downstream of the project, and
4. a project's operational model that typically utilizes a combination of discharge and generation records to compile a water budget.

The preferable approach is to analyze reservoir elevation and spillgate opening records, since these are direct measurements from which spill magnitudes and durations can be calculated. In cases where reservoir elevation and spillgate data are unavailable, alternative approaches can be used to evaluate spill history. Where projects have limited storage capacity, power generation records may be used to determine spills. When generation is offline, flow must be conveyed through bypass valves or over a spillway rather than through turbines. In these cases, generation records can be used in combination with downstream discharge records to characterize spill statistics. However, in some cases flows may be passed through devices for which there are no generation or gate records (e.g., low-flow pipes, sluice gates).

A project's operations model can be used to develop or extend the spill histories for periods in which the model results exhibit good agreement between predicted spills and documented spills (typically telemetric data). An operations model uses a water balance approach of reservoir operations that accounts for flow through the project reservoirs, tunnels, and powerhouse system. A typical operations model includes long-term USGS records, estimates of local inflow from bypass reaches and contributing areas downstream of USGS gages, and a power generation pattern for the project powerhouses developed from recorded generation data. Reservoir spills and magnitudes are typically produced as part of the output from a project's operational model.

3.1.3.1 Selected reference

Stillwater Sciences. 2006. Hydrologic regimes at the Carmen-Smith Hydroelectric Project, upper McKenzie River basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon.

3.1.4 Flow fluctuations

Characterizing flow fluctuations (change in water surface stage) induced by project operations can be particularly relevant for assessing aquatic biological effects such as fish stranding, as discussed in Section 4.2. In addition, if stream channels are composed of unconsolidated material and flow fluctuations are severe, the fluctuations can induce bank instability and erosion. Operational data for characterizing flow fluctuations commonly includes records of reservoir elevation, power generation from the project powerhouses, spillgate and bypass valve openings, inflow from tributaries or other sources, and stage heights and discharges downstream of project dams. Additional, temporary water surface loggers are often deployed in order to monitor flow fluctuations at multiple locations and quantify the downstream extent and magnitude of flow fluctuations.

3.1.5 Synthesis of long-term discharge records

Where possible, long-term flow records from USGS gage data combined with spill and flow diversion records from project facilities can be used to create synthetic long-term regulated and unregulated flow records. However, study reaches are often located in ungaged basins and the USGS gage period of record often does not encompass the complete period of interest (i.e., either the unregulated or regulated periods are not part of the period of record). Therefore, it is often necessary to construct synthetic long-term flow records for regulated and unregulated periods of record in ungaged basins. A common approach to constructing synthetic flow records is to install temporary discharge monitoring stations and correlate these flow records to discharge records from nearby USGS gaging stations. When temporary discharge monitoring stations are not installed, a combination of proration (drainage area relationship between the point of interest and the drainage area of a nearby USGS gaging station) and water budget techniques can be used to construct a synthetic discharge record. Proration techniques between ungaged basins with few or no discharge records and gaged basins with long-term discharge records are appropriate as long as the correlated sites drain similar geologic/geomorphic terrain with similar climate (temperature and precipitation) and land use patterns.

3.1.5.1 Selected reference

Tague, C., and G. E. Grant. 2004. A geological framework for interpreting the low-flow regimes of Cascade streams, Willamette River basin, Oregon. Water Resources Research 40: doi 10.1029/2003WR002629.

3.2.1 Sediment flux

Sediment flux (suspended load or bedload discharge per unit time), estimated from measurements of sediment load in mainstem or tributary channels, is arguably the most reliable metric for evaluating sediment supply to project reservoirs and project-affected reaches. In addition to providing estimates of sediment supply, measured bedload and suspended load flux rates can be used to estimate coarse-to-total load ratios. Bedload sampling technologies include instream installations (e.g., pit traps, net-frame samplers, and detention basins or weir ponds), portable devices (pressure difference samplers, bedload collectors, tracer particles [Figure 2], and scour chains [Figure 3] or cores), and surrogate technologies (acoustic Doppler, hydrophones, gravel impact sensors, magnetic tracers, and topographic differencing). Suspended sediment sampling technologies include single and multi-frequency acoustics, laser defraction, optical sediment flux, digital image analysis, pressure differential, and bulk optics.

The usefulness of existing sediment gaging records for characterizing the longitudinal pattern of sediment supply and extrapolating flux rates to other areas depends on the length of time sediment flux has been monitored and the distribution of monitoring sites relative to geologic terrains, tributaries, and other areas important to sediment production. Correlation of long-term sediment gaging records to flow gaging records is necessary to characterize variability in flux rates over different water year types, especially when projects are located in geomorphic settings characterized by stochastic erosion processes that deliver sediment to channels and mobilize stored channel sediment during large, infrequent triggering events (e.g., large storms, fires, earthquakes, and volcanic eruptions). Short-term gaging records can be correlated to other longterm sediment gaging records if sediment supply is controlled by similar geology, climate, hydrology, and land use.

3.2.1.1 Selected references

Edwards, T. K., and G. D. Glysson. 1999. Field methods for measurement of fluvial sediment. U. S. Geological Survey, Techniques of Water-Resources Investigations, Book 3, Chapter C2.

Gray, R. D., editor. 2003. Proceedings of the Federal Interagency Sediment Monitoring Instrument and Analysis Research Workshop. 9-11 September. Flagstaff, Arizona.

3.2.2 Reservoir sedimentation

Reservoir sedimentation reflects sediment yield from source areas and can be used to estimate average annual unit-area sediment yield. The volume of sediment accumulated in a reservoir since dam construction can be determined using two methods:

1. topographic differencing of reservoir floor elevations through time (e.g., difference between topography prior to sediment filling and current topography) and
2. comparing two area-capacity curves (one based on the reservoir immediately following closure and the other based on current conditions).

Both methods require topographic data for the reservoir basin prior to sediment filling (typically derived from as-built construction drawings) and for current bathymetry. Current bathymetric data are typically useful for a wide range of other resource studies as well as ongoing hydropower operations and maintenance activities. The topographic differencing method has the benefit of describing the spatial distribution of sediment thickness (Figure 4), potentially useful information when evaluating relative sediment yield from geologically and/or geomorphically distinct reservoir source areas (e.g., two rivers flowing in from different geomorphic terrains).

Once the volume of sediment accumulated in a reservoir is determined, the annual unit-area sediment yield to a reservoir can be calculated using the following procedure:

• Accumulated volume is converted to accumulated mass by multiplying by an estimated or measured sediment density.
• Accumulated inorganic mass is estimated based on organic matter content determined from sediment sampled from the project reservoir or nearby reservoirs located in similar terrain.
• Total inorganic mass yield is calculated from accumulated inorganic mass using trap efficiency estimates derived from commonly used empirical equations.
• Average annual, unit-area sediment yield is calculated by dividing the total inorganic mass sediment yield by the reservoir's bedload (regulated) source area and the duration of accumulation.
• Average annual coarse sediment yield (> 2 mm) may be estimated by multiplying the accumulated inorganic mass by a coarse-to-total sediment ratio estimated from suspended load and bedload measurements or from core samples taken from reservoir deposits, and then dividing the total coarse inorganic mass by the reservoir's bedload (regulated) source area and the duration of accumulation.

Coring reservoir deposits is one useful approach for determining parameters that otherwise must be estimated from literature values, including sediment density and grain size distribution, organic matter content, age based on isotope geochronometers (i.e., 137Cs, 7Be, and 210Pb), and correlation of event stratigraphy to floods in the hydrologic record. A coring campaign designed to characterize the age and volume-averaged grain size distribution of reservoir sediment requires an array of sample sites extending the length of a reservoir's longitudinal axis. If the volume averaged grain size distribution of reservoir sediment is determined through coring and laboratory analysis, annual yields can be partitioned by grain size.

3.2.2.1 Advantages and disadvantages of approach

Measuring reservoir sedimentation to examine sediment supply has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages:

• Reservoir sedimentation is a direct measure of the effect of a dam on reducing sediment supply to downstream reaches.
• Large reservoirs efficiently trap sediment supplied by upstream source areas. Estimates of reservoir sedimentation therefore provide a robust measure of sediment yield.
• Reservoir delta deposits often contain event stratigraphy that can be correlated to flood events in the hydrologic record.
• Reservoir sedimentation provides a reliable measure from which to compare estimates of basin sediment yield and/or flux rate derived from other approaches.

Disadvantages:

• Estimates of sediment yield from reservoir sedimentation integrate variability in geomorphic terrains, climate, and changing land use within the reservoir source area.
• Historical topographic data are often coarse (>10 ft contour intervals) and may limit the accuracy of sediment yield estimates.
• Reservoir trap efficiency is commonly estimated from empirical relations with large uncertainty.
• Coring may be cost-prohibitive in large, deep reservoirs.
• Without information about the absolute or relative age of strata within the depositional profile, only the long-term average annual sedimentation rate can be determined based on the total accumulated sediment volume since dam closure. This approach does not account for temporal differences in sediment yield between flood and drought years.

3.2.2.2 Selected references

Ambers, R. 2001. Using the sediment record in a western Oregon flood-control reservoir to assess the influence of storm history and logging on sediment yield. Journal of Hydrology 244: 181-200.

Morris, G. L., and J. Fan. 1998. Reservoir sedimentation handbook: design and management of dams, reservoirs, and watersheds for sustainable use. McGraw-Hill, New York.

Snyder, N. P., D. M. Rubin, C. N. Alpers, J. R. Childs, J. A. Curtis, L. E. Flint, and S. A. Wright. 2004. Estimating accumulation rates and physical properties of sediment behind a dam: Englebright Lake, Yuba River, northern California. Water Resource Research 40.

Stillwater Sciences. 2006. Sediment budget for the Carmen-Smith Hydroelectric Project area, upper McKenzie River basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon.

3.2.3 Extrapolation based on geomorphic processes and rates

Long-term monitoring of sediment flux and field inventory of erosion features required to completely and accurately describe sediment supply is often limited by lack of existing information, the scope of hydroelectric project effects, and the short time-frame encompassed by relicensing studies. A rapid approach to characterizing sediment supply involves extrapolation of geomorphic processes and rates based on terrain modeling, published process rates, analysis of historical aerial photographs, and direct field observations. This approach is commonly employed in source analyses for sediment Total Maximum Daily Load (TMDL) studies.

The rapid approach typically involves the following procedure:

• Characteristics that influence erosion processes (e.g., geology, hillslope gradient, channel gradient, and vegetation cover) are identified and combined in a geographic information system to classify unique terrain types.
• A suite of dominant erosion processes are identified for each terrain type (e.g., shallow landsliding, deep-seated landsliding, soil creep, surface erosion, rockfall, and streambank erosion).
• Unique process rates reported in the literature for regions physiographically similar to the study area are compiled.
• Process rates are standardized to a common unit (e.g., t km-2 y-1 or mm y-1) and averaged to derive a typical average annual rate for each process.
• Sediment production under reference and current conditions is calculated by multiplying each specific terrain area by respective average annual process rates.
• Total production in each subbasin under reference and current conditions is calculated by summing production estimates within each terrain type.

Extrapolation of geomorphic processes and rates to terrains is well-suited where total production and storage estimates in reservoir source areas can be calibrated to reservoir sedimentation rates.

3.2.3.1 Advantages and disadvantages of approach

An extrapolation of sediment supply based on geomorphic processes and rates has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages:

• Geomorphic processes and rates in a drainage basin often cannot be completely inventoried within the limited time frame of a relicensing study. Furthermore, there is often little or no field evidence of historical processes and rates. In these cases, estimates of sediment production and delivery require extrapolation of published process rates and/or sample data. Extrapolation of rates by terrains is a process-based approach that allows flexibility to define terrain types and geomorphic processes according to the unique setting and objectives of an individual study.

Disadvantages:

• Published process rates estimates are often scarce, and application of rates may be somewhat subjective.
• Terrains need to be simplified to a small number of types where geomorphic processes and rates can be sampled in the field and/or from aerial photographs.
• The approach works best in landscapes where well defined terrain characteristics control geomorphic processes.

3.2.3.2 Selected references

Reid, L. M., and T. Dunne. 1996. Rapid evaluation of sediment budgets. Catena Verlag, GMBH, Reiskirchen, Germany.

EPA (U. S. Environmental Protection Agency). 2006. Examples of approved sediment TMDLs

Stillwater Sciences. 2006. Sediment budget for the Carmen-Smith Hydroelectric Project area, upper McKenzie River basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon.

3.2.4 Local sediment sources related to project operation and maintenance

Local sediment sources associated with project facilities should be quantified to determine if they individually and collectively contribute significant amounts of sediment to project-affected stream reaches. Local sediment sources may include erosion features in the vicinity of project dams, spillways, powerhouses, penstocks and canals, project roads and trails, transmission line corridors, and reservoir shorelines (shoreline protection is discussed in Section 8.2). Sequential aerial photography, interviews with operations staff, and field surveys are typically used to map sediment sources and differentiate natural from anthropogenic sediment sources. A field inspection of major project-related sediment sources should be conducted to estimate delivery to water bodies. The field inspection should consist of assessment of the erosion processes and activity level, measurements of each major erosion feature (length, width, and depth), estimation of the grain size distribution of the eroding material, and estimation of sediment delivery to water bodies. The significance of each project-related sediment source should be evaluated based on the relative sediment volumes produced and delivered, the relative sensitivity of channels receiving sediment, and the likelihood of continued sediment production.

3.3.1 Characterization of channel morphology and bed surface texture

Surveys at intensive study sites commonly involve measuring a longitudinal profile of the channel bed along the thalweg and water surface, sediment facies mapping, three or more cross-sections extending onto the floodplain and to the adjacent hillslope toes where feasible, pebble counts conducted at cross-sections to estimate channel roughness and calibrate facies mapping estimates, coarse particle embeddedness and estimation or measurement of armoring ratio, and bulk sampling of surface and subsurface material located in mobile sediment patches.

3.3.1.1 Advantages and disadvantages of approach

Characterizing channel morphology and bed surface texture to measure sediment transport and channel condition has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages:

• Channel geometry and bed surface data are valuable components to multiple studies including sediment transport modeling, hydrologic studies, and fisheries studies.
• A coarse-level analysis facilitates selection of intensive study sites and provides additional data that can be used to characterize the geomorphology of the study area.
• Monumented cross-sections and longitudinal profiles are repeatable and provide excellent baseline data for future monitoring efforts.
• Sediment facies, pebble counts, and bulk samples provide a multi-faceted approach to characterizing local and reach-scale channel grain size composition.

Disadvantages:

• Without historical data (e.g., channel geometry and grain size information), it is difficult to quantify changes in channel condition with respect to historical conditions and therefore potential ongoing project effects.
• Mapping sediment facies onto aerial photographs relies on visual estimates of channel grain distributions and must be consistently conducted by the same individual in order to minimize observer bias.
• Bulk sampling in high gradient, mountainous streams that are dominated by coarser bed material may be infeasible.

3.3.1.2 Selected references

Buffington, J. M., and D. R. Montgomery. 1999. A procedure for classifying textural facies in gravel-bed rivers. Water Resources Research 35: 1903-1914.

Bunte, K., and S. R. Abt. 2001. Sampling surface and subsurface particle-size distributions in wadable gravel- and cobble-bed streams for analyses in sediment transport, hydraulics, and streambed monitoring. General Technical Report No. RMRS-GTR-74. USDA Forest Service, Fort Collins, Colorado.

Montgomery, D. R., and J. M. Buffington. 1997. Channel-reach morphology in mountain drainage basins. Geological Society of America Bulletin 109: 596-611.

Montgomery, D. R., and J. M. Buffington. 1998. Channel processes, classification, and response. Pages 13-42 in R. J. Naiman and R. E. Bilby, editors. River ecology and management. Springer-Verlag, New York.

3.3.2 Bedload transport

Bedload transport creates and modifies bedform topography, controls sediment storage, affects surface texture through selective transport and abrasion, influences channel migration, and directly influences aquatic habitat. The flux rate of coarse material is an important component of sediment mass balance within a regulated reach. Higher bedload transport capacity can lead to greater potential geomorphic impacts of reduced coarse sediment supply.

Bedload transport is typically modeled and calibrated with field studies at intensive study sites to estimate surface-based dimensionless Shield stress, critical discharges to mobilize the channel bed, coarse (> 2 mm) bedload transport capacity, and bedload grain size distributions. Model input parameters commonly include channel cross-section data, water surface slope, grain size (channel roughness) data of either the channel surface substrate or the bedload supply, and annual flow duration curves of the current and reference flow regimes. Model output parameters commonly include Shields stress versus discharge rating curves, average annual coarse bedload transport capacity, and grain size distributions of either the bedload supply or channel surface (depending on whether the input parameter was surface or bedload supply grain size). Long-term synthetic hydrologic flow records representing current and reference conditions may be used to generate flow duration curves for modeling bedload transport capacity. To calibrate the reference Shields stress used for sediment transport modeling, marked tracer rocks with grain size approximately equal to the local surface D50 and D84 may be placed at each cross-section to identify thresholds of bed mobility (Figure 2). Tracer rocks are generally placed in a line along previously surveyed cross-sections and monitored after high flow events.

3.3.2.1 Advantages and disadvantages of approach

Modeling bedload transport to measure sediment transport and channel condition has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages:

• Numerical modeling of bedload transport capacity provides a method for evaluating the effects of changes between the current and reference flow regime on sediment transport.
• Modeling annual bedload transport capacity provides a metric to assess the mass sediment balance between supply and transport.
• Tracer rocks provide a direct observation of bed mobility.

Disadvantages:

• There is generally a high degree of uncertainty in bedload transport modeling, which increases in higher gradient, boulder dominated streams where large roughness elements create significant deviations in shear stress and limit the effectiveness of bedload transport equations based on total boundary shear stress.
• In order for tracer rock studies to provide relevant data, a high flow event great enough to mobilize the particles must occur during the study period.
• Tracer rock studies generally do not provide continuous data (unless radio-tagged or other emitters are employed), and thus the precise discharge level that mobilized the particles during a storm event cannot be determined.

3.3.2.2 Selected references

Buffington, J. M., and D. R. Montgomery. 1997. A systematic analysis of eight decades of incipient motion studies, with special reference to gravel-bed rivers. Water Resources Research 33: 1355-1380.

Mueller, E. R., J. Pitlick, and J. M. Nelson. 2005. Variation in the reference Shields stress for bed load transport in gravel-bed streams and rivers. Water Resources Research 41: W04006, doi: 10.1029/2004WR003692.

Parker, G. 2006. Transport of gravel and sediment mixtures. Draft revised Chapter 3 of V. A. Vanoni, editor. 1975. Sedimentation engineering. ASCE Manual 54. American Society of Civil Engineers, New York.

3.3.3 Fine sediment accumulation

In regulated reaches with abundant supply of fine sediment, decreased peak flow magnitude and/or frequency may increase fine sediment accumulation in pools and in gravel interstices, affecting the quality of stream habitat for fish and other aquatic species. Fine sediment (< 2 mm) accumulation in project-affected reaches (e.g., bypass reaches) can be evaluated by

1. bulk sediment samples from the bed surface and subsurface to determine fine sediment concentration, and
2. V* (proportion of residual pool volume occupied by mobile fine sediment) or equivalent techniques for estimating fine sediment deposition in pools.

The V* technique is applicable in reaches with pool-riffle morphology, stable banks, channel gradient less than 5%, and wadable pools. Selected pools must have a definable riffle crest (a pool's hydraulic control and usually the shallowest place at the downstream end of a pool), which excludes pools formed by LWD or boulder dams. In certain cases, a modified V* approach that allows for a greater number of pools to be sampled over a given time period, may be more advantageous to complete the study's objectives. Examples of modified V* methodologies include Stillwater Sciences' streamlined V* (Stillwater Sciences 2006) and S* developed by the Sierra National Forest (USDA Forest Service 1997). Both of these simplified methodologies have shown good correlation with the full V* method of Hilton and Lisle (1993) where both methods are used to characterize the same pool.

3.3.3.1 Advantages and disadvantages of approach

Measuring fine sediment accumulation with the V* method to investigate sediment transport and channel condition has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages:

• The systematic V* approach is simple, repeatable, and statistically unbiased. Hilton and Lisle (1993) found that when V* measurements were repeated by different observers, the standard deviation from the mean pool V* was less than 20% for pools with moderate to high sediment volumes, but that the standard deviation increased significantly for pools with small fine sediment volumes.
• Simplified V* approaches allow rapid collection of data on multiple pools, which can facilitate pool inventories in multiple reaches.

Disadvantages:

• The V* method only characterizes fine sediment accumulation in pools and does not address fine sediment deposition in riffles. Various other methods (e.g., sediment facies mapping, pebble counts, particle embeddedness, and bulk samples of surface and subsurface material) may be necessary to assess fine sediment accumulation in locations outside pools.
• V* measurements taken during one sampling season may not represent fine sediment characteristics during other seasons or years.
• Direct comparison of pre- and post-project fine sediment accumulation is often not possible because information about pre-project fine sediment accumulation is not available. Flushing flow experiments have been conducted to simulate pre-project fine sediment conditions.
• V* measurements are strongly influenced by the volume and grain size distribution of local sediment sources (i.e., bank erosion or shallow landsliding) that may not be project-related or indicative of the pools within the reach.

3.3.3.2 Selected references

Hilton, S., and T. E. Lisle. 1993. Measuring the fraction of pool volume filled with fine sediment. Research Note PSW-RN-414. USDA Forest Service, Pacific Southwest Research Station, Berkeley, California.

Stillwater Sciences. 2006. Fluvial geomorphic processes and channel morphology at the Carmen-Smith Hydroelectric Project area, upper McKenzie River Basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon.

USDA Forest Service. 1997. A reconnaissance level indicator of pool fine sediment. Sierra Nevada Forest, Kings River Ranger District, California. Unpublished report.

3.3.4 Distribution of side channels

Project effects on LWD loading, sediment supply, active channel storage, and peak flows may reduce connectivity to side channels, as well as their extent and stability. Reduced peak flow magnitude and/or frequency may also impact the functionality of side channels by reducing access to flow. Methods for evaluating project effects on the distribution, frequency, and length of side channels includes analysis of an aerial photographic time series and field inventories of side channels during low flow. Field inventories may include evaluation of mechanisms of side channel formation (e.g., LWD, channel and/or valley morphologic controls, or sediment deposition), vegetation age on the island bars or terraces between the side channel and main channel, stability of the side channels, and connectivity with the main channel. At the inlet and outlet controls (minimum elevation for surface water from the main channel to connect with the side channel) of the side channels, differential leveling may be used to survey the local water surface and thalweg elevations of the main and side channels to assess topographic controls on surface water flow connectivity with the main channel. Cross-sections and channel roughness data at side channel inlets can also be surveyed as input parameters for water surface modeling aimed at estimating stage-discharge thresholds for surface flow connectivity.

Assessing the distribution of side channels should consider the following:

• Historical aerial photographs can be a useful tool for assessing change in side channel frequency and length.
• Field inventories of extent and stability of side channels provide additional information on side channels within the project area that cannot be determined from aerial photographs and also provide a metric to calibrate side channel extents estimated from historical photographs.
• Topographic surveys of the elevations of the inlet and outlet controls of the side channel relative to the main channel provides data to assess surface flow connectivity with the main channel and the potential effects of altered flow regimes on surface flow connectivity.
• In highly confined or densely vegetated reaches (particularly if aerial photographs are shot while deciduous vegetation is leafed out), side channels can be difficult to detect.
• Without water surface modeling and/or field observations during multiple flow stages, side channel connectivity to the main channel can be difficult to reliably determine.

4.1.1 Introduction

The quantity, complexity, and quality of riverine habitat available for aquatic species depend to a large extent on the timing, frequency, duration, rate of change, and magnitude of instream flows. These flows vary seasonally and annually, and are affected by flow alterations related to project operations. Results of instream flow studies can be used to evaluate potential beneficial or negative effects of current and proposed instream flow regimes on habitat for life stages of analysis species. Traditionally used approaches to studying instream flows, as well as newly applied approaches, are discussed below, including IFIM and one-dimensional (1D) PHABSIM, two-dimensional (2D) hydrodynamic modeling, habitat criteria mapping, expert habitat mapping, macroinvertebrate community assessments, and flow prescriptions (methods to assess hydroelectric project effects on hydrology, including identifying natural hydrograph components, are discussed above in Section 3.1). These approaches were selected for evaluation because they are commonly used, and/or have been successful at providing relicensing participants with the information needed to select appropriate flows.

Many additional approaches to evaluating instream flows are available, including the following methods evaluated in detail in Annear et al. (2004):

• Indicators of Hydraulic Alteration (IHA)
• Range of Variability Approach (RVA)
• New England Aquatic Base Flow (ABF) Standard
• Biological Response to Flow Correlation Method
• Feeding Station Method
• Flow Duration Curve Methods
• Index of Biological Integrity (IBI)
• Target Fish Community Assessment
• MesoHABitat SIMulator (MesoHABSIM)
• Hatfield-Bruce Western Salmonid Regressions
• The Pennsylvania/Maryland Instream Flow Model
• Plunge Pool Method
• Riverine Community Habitat Assessment and Restoration Concept (RCHARC) Method
• Single Transect Hydraulic-Based Habitat Methods
• Tennant Method
• Washington Toe-of-Bank-Width Method (Toe-Width Method)
• Wetted Perimeter
• Channel Maintenance Flows in Gravel-Bed Streams
• Seven-day, ten-year low flow (7Q10)
• Floodplain Inundation Method
• Migration Cue Method
• Demonstration Flow Assessment (DFA) Method

All of the methods listed and discussed are only useful if they are applied to specific and appropriate questions. Many of the disadvantages of these approaches can be avoided by clearly identifying the questions for the project, and applying the methods in a directed way. In addition, these approaches are typically more successful when used in conjunction with other approaches.

The Instream Flow Council website provides detailed information on instream flow methods, including case histories, key considerations, bibliographies, and related issues.

Limitations associated with all instream flow approaches include:

• Measurement and sampling problems in developing habitat suitability curves or habitat criteria. Suitability criteria are also often biased because they are based on site-specific habitat conditions and use of vertically-averaged velocities, and the criteria fail to account for habitat preferences that vary based on the scale that is considered. For example, the focal point (or "nose") water velocities used by a fish are often much lower than the average water velocity at the same location.
• Lack of information on how organisms might select habitat differently with different species assemblages (e.g., effects of competition and predation).
• Little data on winter habitat use (data have most often been collected in other seasons)
• Uncertainty regarding which physical or biological characteristics species actually use to select habitat (i.e., habitats that appear to be similar may not be used with equal emphasis).
• Generally limited to mapping those characteristics that can be easily measured in a repeatable manner (e.g., depth, velocity, substrate size), so may rely heavily on assumption that organisms are selecting habitat based on those characteristics.
• Inability to detect subtle differences in habitat, such as velocity gradients, based on the resolution of studies.

4.1.1.1 Selected references

Annear, T., I. Chisholm, H. Beecher, A. Locke, P. Aarrestad, N. Burkhart, C. Coomer, C. Estes, J. Hunt, R. Jacobson, G. Jobsis, J. Kauffman, J. Marshall, K. Mayes, C. Stalnaker, and R. Wentworth. 2004. Instream Flows for Riverine Resource Stewardship, revised edition. Instream Flow Council, Cheyenne, WY.

Arthington, A. H., and M. J. Zalucki. 1998. Comparative evaluation of environmental flow assessment techniques: review of methods. Land and Water Resources Research and Development Corporation, Canberra, Australian Capitol Territory.

EA Engineering, Science, and Technology,. 1986. Instream flow methodologies. Final Report EA-4819, Project 2194-2. Prepared for Electric Power Research Institute by EA Engineering, Lafayette, California.

Jowett, I.G., 1997: Instream flow methods: a comparison of approaches. Regulated Rivers 13. 115-127.

Kondolf, G. M., E. W. Larsen, and J. G. Williams. 2000. Measuring and modeling the hydraulic environment for assessing instream flows. North American Journal of Fisheries Management 20: 1016-1028.

Railsback, S. 2001. Instream flow assessment methods: guidance for assessing instream flow needs in hydropower relicensing. Electric Power Research Institute, Palo Alto, California.

4.1.2 IFIM and one-dimensional (1D) PHABSIM

The instream flow incremental methodology (IFIM) and one-dimensional (1D) physical habitat simulation (PHABSIM) modeling are standard approaches to assessing instream flow needs for aquatic species (Figure 5). The first step is to perform a detailed stream or aerial survey, or map habitats, in the study area to determine the extent and distribution of habitat types. Following habitat mapping, individual study reaches and instream flow transect locations are established. Hydraulic and habitat data are collected at each transect using standard techniques employed in instream flow studies. The transect data are then processed through hydraulic simulation submodels within the PHABSIM model, generating simulations of depth and velocity distributions over a broad range of flows. Literature-derived or site-specific habitat suitability criteria (HSC) are applied to the predicted hydraulic parameters to produce functional relationships between flow and aquatic habitat (expressed as weighted usable area, or WUA). Lastly, a habitat time series analysis is performed to integrate WUA results across spatial (reach-long) and temporal (over the hydrologic period of record) scales.

4.1.2.1 Advantages and disadvantages of approach

Use of IFIM and one-dimensional (1D) PHABSIM to assess instream flows has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• Measurement approach at transects is standardized, widely used, and repeatable.
• The level of precision in the results can be adjusted by altering sampling intensity.
• Other studies can utilize data collected at transects, including studies on potential fish stranding, hydrology, or fluvial geomorphic processes.
• Multiple habitat values (depth, velocity, substrate, and cover) can be simultaneously accounted for.
• Limited professional judgment is required for input data, with the exception of selecting habitat suitability criteria.
• Habitat criteria values, or analysis species, can be updated or added to the analysis as new information becomes available, without collecting additional field data.
• Incremental approach allows habitat assessments to be conducted at any simulated flow (although it is most accurate within the range of measured flows).

Disadvantages

• There are sampling issues associated with using data collected at transects to represent river reaches. There is no ability to account for conditions upstream or downstream of transects, and therefore transect location heavily influences results. Unless the transects are representative of the remainder of the river, small biases (e.g., particularly low or high amount of habitat at one location) in the results at one transect are multiplied during the extrapolation. The more complexity in a river system, the greater the risk of bias. This is typically addressed by increasing the number of transects in complex (e.g. high gradient) systems.
• There is limited ability to address hydraulic conditions where the water surface elevations vary across a transect (e.g., split channels, and high gradient riffles).
• Can only simultaneously account for a limited set of habitat values (depth, velocity, and a channel index such as substrate or cover).
• Hydraulic modeling typically occurs at a coarser scale than that at which organisms respond to their hydraulic environment; a mis-match in scale occurs when combining results from hydraulic models with habitat suitability or preference data collected on a finer scale. Suitability criteria are also often biased because they are based on site-specific habitat conditions and use of vertically-averaged velocities, and the criteria fail to account for habitat preferences that vary based on the scale that is considered. For example, the focal point (or "nose") water velocities used by a fish are often much lower than the average water velocity at the same location.
• There is a weak tie to population response, and interpretation of results almost always assumes that minimum flows limit the abundance and/or distribution of populations. There is a limited ability to integrate results with a limiting factors analysis, so discerning which species or life-stage should drive flow selection is unreliable. Does not provide total amount of preferred or usable habitat available at varying flows, so the data can not be used in population modeling (see Section 4.6).
• Integrating WUA results with other analyses (e.g. limiting factors analysis) is problematic, since the metric serves mostly as a relative index to compare various flows.
• Application of the model requires professional judgment regarding how well the habitat portion of the model actually fits what is being modeled.
• Does not allow calculations of statistical error bounds on the predicted habitat-flow relationships, so the reliability of the results cannot be estimated and considered when making management decisions.

4.1.2.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• 1D PHABSIM models rely on the assumption of a simple channel with either gradual variation in flow or uniform flow, which is atypical for some habitat types.
• Not reliable in hydraulically complex areas due to limited ability to address spatial shifts in water velocity as flows change. IFIM and 1D approaches are best applied in systems without substantial bed roughness, or without hydraulic complexity.
• Has not been widely applied in spring-dominated streams, and may not adequately address aquatic habitats there.
• In study areas with long stream reaches, or a variety of stream channels (e.g., side channels) to be assessed, an extensive number of transects are needed to adequately characterize habitat-flow relationships.
• Works well in deep pools that have consistent average velocities, but if pools are hydraulically complex, the results are less reliable.
• Extensive data collection can be very expensive.
• Has been applied at many locations throughout the world, including high-gradient and multi-channel streams, as well as warmwater streams throughout the United States. The following link provides a list of contacts familiar with examples in their region, accessible by clicking on the state or province on the map.

4.1.2.3 Selected references

Bovee, K.D., B.L. Lamb, J.M. Bartholow, C.B. Stalnaker, J. Taylor, and J. Henriksen. 1998. Stream Habitat Analysis Using the Instream Flow Incremental Methodology. Fort Collins, CO: U.S. Geological Survey-BRD. Information and Technology Report USGS/BRD/ITR-1998-0004. 130 p.Parasiewicz, P. 2001. MesoHABSIM: a concept for application of instream flow models in river restoration planning. Fisheries 26: 6-13.

Castleberry, D. T., J. J. Cech, Jr., D. C. Erman, D. Hankin, M. Healey, G. M. Kondolf, M. Mangel, M. Mohr, P. B. Moyle, J. Nielsen, T. P. Speed, and J. G. Williams. 1996. Uncertainty and instream flow standards. Fisheries 21: 20-21.

Milhous, R.T. 1998. Application of the principles of IFIM to the analysis of environmental flow needs for substrate maintenance in the Trinity River, northern California. In: Hydroecological Modelling: Research, practice, legislation, and decision-making. Praha, Czech Republic: T.G. Masaryk Water Research Institute. p. 50-52.

Milhous, R. T., D. L. Wegner, and T. Waddle. 1984. User's guide to the Physical Habitat Simulation System (PHABSIM). Instream Flow Information Paper No. 11, FWS/OBS-81/43 Revised. Prepared by Instream Flow and Aquatic Systems Group, U. S. Fish and Wildlife Service, Fort Collins, Colorado and U. S. Bureau of Reclamation, Upper Colorado Region, Salt Lake City, Utah for U. S. Fish and Wildlife Service, Washington, D. C.

Nakamura, S., and T. J. Waddle. 1999. IFIM Nyuumon (Translation of two documents into Japanese: The Instream Flow Incremental Methodology - A Primer for IFIM and Stream Habitat Analysis Using the Instream Flow Incremental Methodology). Tokyo, Japan: Technology Center for Riverfront Development. 197 p.

Railsback, S. 1999. Reducing uncertainties in instream flow studies. Fisheries 24: 24-26.

Stalnaker, C.B. 1998. The Instream Flow Incremental Methodology. In: Hydroecological Modelling: Research, Practice, Legislation and Decision-Making. Prah, Czech Republic: T. G. Masaryk Water Research Institute. p. 9-11.

Stalnaker, C.B., B.L. Lamb, J. Henriksen, K. Bovee, and J. Bartholow. 1995. The Instream Flow Incremental Methodology: A Primer for IFIM. Washington, DC: U.S. Geological Survey. Biological Report 29. 45 p.

Van Winkle, W., C. C. Coutant, H. I. Jager, J. S. Mattice, D. J. Orth, R. G. Otto, S. F. Railsback, and M. J. Sale. 1997. Uncertainty and instream flow standards: perspectives based on hydropower research and assessment. Fisheries 22: 21-22.

WDFW and WDOE (Washington Department of Fish and Wildlife and Washington Department of Ecology). 2004. Instream flow study guidelines: technical and habitat suitability issues. WDFW and WDOE, Olympia, Washington.

The following link provides additional information on instream flow incremental methodology: USGS (U. S. Geological Survey). 2003. Instream Flow Incremental Methodology (IFIM). U.S. Department of Interior, USGS, Fort Collins Science Center, Fort Collins, Colorado.

4.1.3 Two-dimensional (2D) hydrodynamic modeling

The two-dimensional (2D) hydrodynamic modeling approach consists of:

1. generating detailed digital terrain models (DTM) of the study sites (Figure 6),
2. collecting substrate and cover data to create polygons to overlay onto the DTMs for modeling hydraulic roughness and for modeling aquatic habitat,
3. collecting water surface calibration data, and
4. 2D modeling of flow fields over a range of flows.

The 2D modeling in turn consists of:

1. selecting a 2D hydrodynamics model,
2. generating computational meshes,
3. water surface modeling, and
4. velocity and depth modeling.

A number of two-dimensional flow models are used for analysis (FESWMS, River2D, Mike21, etc.), and new models are continually being created and adapted to address the concerns listed below. In general, the models are incorporated into a multi-dimensional surface modeling system, based on three-dimensional riverbed topography, flow rate, and downstream stage (i.e., water surface elevations) boundary conditions to calculate flow, velocities, water surface elevations, and boundary shear stresses in the channel. These have been used in channels with or without islands in both high and low Froude number flows (i.e., sub-critical and super-critical flow conditions).

The 2D modeling approach uses habitat criteria values (typically depth, velocity, and cover) from the literature in the same manner as IFIM and PHABSIM to determine the habitat-flow relationship for analysis species and life stages for the study reach. See Section 6.4.3 for a discussion of the use of 2D modeling to assess instream flows for amphibians.

4.1.3.1 Advantages and disadvantages of approach

Use of 2D modeling to assess instream flows has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• Approach requires intensive collection of topographical data, and thus no extrapolation between transects is required.
• Can account simultaneously for multiple habitat values (depth, velocity, substrate, and cover).
• Allows modeling of any simulated flows (within range of measured flows) and as many species and life stages as needed.
• Species habitat criteria can be changed and the sites can be remodeled if habitat criteria information is updated.
• Standardized application, which is also repeatable.
• Results in a highly visual output that is easy to interpret.

Disadvantages

• All water velocity measurements are based on vertically-averaged water velocities, which often do not represent locations where aquatic species hold or feed.
• Although it can account simultaneously for multiple habitat variables, it is difficult to account for additional metrics, such as the focal velocity of an organsims that resides on the substrate.
• Hydraulic calibration of the model emphasizes mass balance, and there is little confirmation of the accuracy of velocity or depth simulation.
• This approach uses habitat suitability criteria which are often biased because they are based on site-specific habitat conditions and use of vertically-averaged velocities, and the criteria fail to account for habitat preferences that vary based on the scale that is considered. For example, the focal point (or "nose") water velocities used by a fish are often much lower than the average water velocity at the same location.
• There is a weak tie to population response, and interpretation of results almost always assumes that minimum flows limit the abundance and/or distribution of populations. There is a limited ability to integrate results with a limiting factors analysis, so discerning which species or life-stage should drive flow selection is unreliable. Does not provide total amount of preferred or usable habitat available at varying flows, so the data can not be used in population modeling (see Section 4.6).
• Does not allow clarification of statistical error bounds on the predicted habitat-flow relationships; therefore the reliability of the results can not be estimated and considered when making management decisions.

4.1.3.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• 2D models are less reliable in hydraulically complex areas due to poor ability to address spatial shifts in water velocity. 2D approaches are best applied in systems without substantial bed roughness, or without hydraulic complexity. Increasing the precision of the topography can compensate for errors when applied in systems with substantial bed roughness.
• The density of the mesh screen used to generate topography affects accuracy of results. With adequate mesh densities, has the ability to model hydraulics accurately.
• Cannot be applied to a larger area than is modeled. Study reaches tend to be short. A total habitat area for the reach is not estimated.
• Intensive data collection can be very expensive.
• Has been applied on the Oak Grove Fork of the Clackamas River at the Clackamas River Hydroelectric Project (FERC Project No. 2195), Oregon; at the Klamath Reclamation Project, on the Klamath River (FERC Project No. 2082), California; on LaVerkin Creek, Utah; on the Pit River Hydroelectric Project (FERC Project No. 2687) on the Pit River, California; and on the Spring Lake and San Marcos River system, Texas.

4.1.3.3 Selected references

Addley, R.C. and J.A. Ludlow 2001. Kerr Dam Ramping Rate Study Lower Flathead River. Final Report for the Confederated Salish and Kootenai Tribes. Utah Water Research Lab, Utah State University, Logan, Utah. 86pp.

Hardy, T.B. and Addley, R.C. 2001. Evaluation of interim instream flow needs in the Klamath River, Phase II Final Report (draft). Institute for Natural Systems Engineering, Utah State University.

Hardy, T. B., and R. C. Addley. 2003. Instream flow assessment modelling: combining physical and behavioural-based approaches. Canadian Water Resources Journal 28: 273-282.

Nelson, J.M. 1996. Predictive Techniques for River Channel Evolution and Maintenance. Water, Air and Soil Pollution 90:321-333.

Nelson, J.M. and J.D. Smith. 1989. Flow in meandering channels with natural topography, in River Meandering, Water Resour. Monog., Vol. 12, edit by S. Ikeda and G. Parker, pp. 69-102, AGU, Washington, D.C.

Steffler, P., and J. Blackburn. 2002. River 2D: two-dimensional depth averaged model of river hydrodynamics and fish habitat. Introduction to depth averaged modeling and user's manual. Prepared by University of Alberta.

Thompson, D.M., Nelson, J.M., and Wohl, E.E., 1998, Interactions between pool geometry and hydraulics: Water Resources Research, v. 34, no. 12, p. 3673-3681.

The following link provides additional information on Two-Dimensional (2D) Hydrodynamic Modeling. Search with keywords "Two-Dimensional Hydrodynamic Modeling".

4.1.4 Habitat criteria mapping

Habitat criteria mapping is a relatively new approach that relies on ground-based mapping of available habitat within representative mesohabitat units (e.g., pool, riffle, run) for the species and life stages of interest at a specified range of flows, rather than a modeling approach based on extrapolation from transects. The habitat mapping approach involves mapping and quantifying preferred habitat for specific life stages of a selected group of "analysis species" and life stages in the study area. Criteria used to determine preferred habitat are based on values from the scientific literature for each species and life stage selected for analysis, as well as by collaboration with stakeholders and species experts. Habitat criteria values in the literature are reviewed for their applicability to the study area and to the populations and assemblages found there, and an appropriate range of values are selected. The approach can be applied in a very similar manner to MesoHABSIM (Parasiewicz 2001), or at finer spatial scale.

The habitat criteria mapping approach relies on ground-based measurements in the field and mapping of preferred habitat on digitally rectified low-elevation aerial photographs for a sub-sample of habitat units (e.g., pool, riffle, run). Suitable habitat is delineated in the field using well-defined habitat criteria for the species and life stages of interest in selected habitat units at various flows (Figure 7). The resulting polygons are transferred into a GIS framework to calculate available habitat area for each analysis species and life stage for each measured flow. Available habitat area is then extrapolated to similarly classified habitat units in the study area to estimate total habitat availability within the reach with an associated estimate of variance.

4.1.4.1 Advantages and disadvantages of approach

Use of habitat criteria mapping to assess instream flows has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• Examines the entire reach for habitat, rather than potentially biased cross sections.
• Accepts variable quantities of input data for variable levels of accuracy.
• By estimating total area available at each flow (rather than an index), the approach allows the results of the habitat mapping to be used in population models to determine habitat-based production within a limiting factors framework by quantifying estimates of habitat area for key life stages under different flows. This provides the ability to evaluate potential population responses to changes in instream flows (e.g., effects of doubling spawning habitat while decreasing juvenile rearing habitat).
• Measurements in the field do not average water velocities, and can account for substrate-oriented organisms (e.g., bull trout) separately from mid-column ones (e.g., cutthroat trout).
• Mapping is based on habitat criteria derived from the best available information from the scientific literature and expert opinion, and is repeatable.
• It is possible to determine measurement error, and to estimate the variance of all habitat estimates.
• Compatible with calibration and validation by use of direct observation snorkel dives in areas mapped as preferred or not preferred.

Disadvantages

• Based on suitability criteria, which are often biased because they are based on site-specific habitat conditions and use of vertically averaged velocities, and they fail to account for habitat preferences that vary based on the scale that is considered.
• Can only analyze flows that are studied empirically, and cannot simulate habitat flow relationship other than measured flows.
• Does not allow for adjustment after data collection if new information regarding selected habitat criteria becomes available.

4.1.4.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• Can be applied accurately in hydraulically simple or complex streams. Therefore, it works well in high-gradient, boulder-dominated systems, where other methods do not work as well. However, it does not work well in areas that are too deep to wade safely.
• By using mesohabitats as sampling units, the approach is able to estimate the relationship between flow and habitat for long river reaches.
• Requires intensive, and costly, field data collection.
• Has been applied at the Carmen-Smith Hydroelectric Project (FERC Project No. 2242), on the McKenzie River, Oregon.

4.1.4.3 Selected references

Parasiewicz, P. 2001. MesoHABSIM: a concept for application of instream flow models in river restoration planning. Fisheries 26: 6-13.

Stillwater Sciences. 2006. Aquatic habitats and instream flows at the Carmen-Smith Hydroelectric Project, upper McKenzie River basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon.

Vadas, R. L., Jr., and D. J. Orth. 1997. Species associations and habitat use of stream fishes: the effects of unaggregated-data analysis. Journal of Freshwater Ecology 12: 27-37.

Vadas, R. L., Jr., and D. J. Orth. 2000. Habitat use of fish communities in a Virginia stream system. Environmental Biology of Fishes 59: 253-269.

4.1.5 Expert habitat mapping

The expert habitat mapping approach is another relatively new approach that is very similar to the habitat criteria mapping approach with one key distinction. Rather than mapping polygons of preferred habitat based on habitat criteria values from the literature, the expert habitat mapping approach relies on a combination of field experience, insight, and quantitative habitat criteria. Although the output, and ability to extrapolate to long river reaches is similar to habitat criteria mapping, this one distinction results in different advantages and disadvantages, as described below.

4.1.5.1 Advantages and disadvantages of approach

Use of expert habitat mapping to assess instream flows has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• Examines the entire reach for habitat, rather than potentially biased cross sections.
• Criteria for mapping are not based on potentially biased suitability criteria, although professional judgment is used during the mapping of polygons.
• Because mapping criteria are not limited by specific measured physical criteria, it allows the simultaneous consideration of an array of qualitative and quantitative factors influencing habitat, including shear zones, vertical velocities, cover, and professional judgment.
• Does not average water velocities, and can account for substrate oriented organisms (e.g., bull trout) separately from mid-column oriented ones (e.g., cutthroat trout).
• By estimating total area available at each flow (rather than an index), the approach allows the results of the habitat mapping to be used in population modeling efforts to determine habitat-based production within a limiting factors framework by quantifying estimates of habitat area for key life stages under different flows. This provides the ability to evaluate potential population responses to changes in instream flows (e.g., effects of doubling spawning habitat while decreasing juvenile rearing habitat).
• Compatible with calibration and validation by use of direct observation snorkel dives in areas mapped as preferred or not preferred.
• Effective at building a consensus to accept results of analysis by including stakeholders in data collection.
• Relatively fast, and thus allows long reaches to be surveyed.

Disadvantages

• Possible bias, due to differences in interpretation of habitat suitability and preference among experts.
• Can only analyze flows that are studied empirically, and cannot simulate habitat flow relationship beyond measured flows.
• Cannot determine statistical error bounds on predicted habitat-flow relationship.
• Does not allow for adjustment after data collection if new information regarding selected habitat criteria becomes available.
• The approach is not repeatable, although it may be possible to determine measurement error, and variance of habitat area estimates.
• Difficult to test and calibrate; requires experts who may be difficult or expensive to include in the process.

4.1.5.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• Can be applied in hydraulically simple or complex streams. Therefore it works well in high-gradient, boulder-dominated systems, where other methods do not work as well. However, it does not work well in areas that are too deep to wade safely.
• By using mesohabitats as sampling units, the approach is able to estimate the relationship between flow and habitat for long river reaches.
• Works best when a process is established to resolve potential disagreements among experts, and when a collaborative "expert" report is produced to avoid disputed conclusions.
• Has been applied on the Oak Grove Fork of the Clackamas River at the Clackamas River Hydroelectric Project (FERC Project No. 2195), Oregon; and at the Blue Lake Hydroelectric Project (FERC Project No. 2230), on Sawmill Creek, Alaska.

4.1.5.3 Selected references

McBain and Trush. 2003. Estimating salmonid habitat availability in the lower Oak Grove Fork using expert habitat mapping: summary of methods and preliminary results. Prepared for Clackamas Instream Flow/Geomorphology Subgroup, Portland General Electric, Portland, Oregon by McBain and Trush, Arcata, California.

Morhardt, J. E., D. F. Hansen, and P. J. Coulston. 1983. Instream flow: increased accuracy using habitat mapping. Ecological Analysts, Inc., Lafayette, California.

Stanfield, L. W., and M. L. Jones. 1998. A comparison of full-station visual and transect-based methods of conducting habitat surveys in support of habitat suitability index models for southern Ontario. North American Journal of Fisheries Management 18: 657-675.

4.1.6 Macroinvertebrate community assessment

The abundance and composition of benthic macroinvertebrates are influenced by stream flow that in turn may be affected by Project operations; thus, benthic macroinvertebrates may provide an indirect indication of aquatic habitat integrity in relation to instream flows (as well as flow fluctuations, as described in Section 4.2.4). Assessments are usually conducted to evaluate impacts that have occurred, rather than to prescribe future desired conditions, or mitigation measures. There are two main approaches to assessing the effects of instream flows on macroinvertebrate communities. Of these approaches, the index of biotic integrity (IBI) approach (Karr and Chu 1997, Karr 1999) is more typically employed for instream flows studies, while the functional feeding group (FFG) approach (Cummins and Klug 1979) has been utilized for benthic macroinvertebrate community alteration assessments in relation to land management and more recently for instream flows.

In the FFG approach, collected samples are typically sorted in the field into functional feeding groups according to the classification system developed by Cummins and Klug (1979), later modified by Merritt and Cummins (1996). The separation of macroinvertebrates into FFGs is based on the mechanisms by which they acquire food; the morphological and behavioral adaptations for acquiring food are readily observed in the field with live, freshly collected specimens. For example, shredders often have generalized mouthparts for tearing pieces of matter from larger materials, whereas scrapers have modified mouthparts, such as slightly cupped mandibles with brush-like structures at the base that allow them to scrape food from rocks. Filtering collectors have specific body modifications such as filtering hairs on forelegs, or behavioural mechanisms such as net-spinning to collect fine particles suspended in the water. The composition of these FFGs can then be used to characterize potential effects of a hydroelectric project. Though this method is relatively easy and inexpensive, information gained is qualitative, and may not provide the data necessary to make strong inferences about the effect of a given hydroelectric project on the macroinvertebrate community. Although sorting is conducted in the field, laboratory analyses of selected samples is usually conducted to validate the field counts and to calculate fish drift-feeding indices.

For the IBI approach, just as with the FFG approach, substrate is sampled using a mesh collection net or artificial substrate. However, instead of sorting specimens in the field as with the FFG approach, samples are preserved and processed in the laboratory. Representative sub-samples are generally identified to family, with identification to genus or species as required and/or feasible. Using these identifications, assemblage composition is assessed by calculation of metrics that are based on the presence/absence and abundance of individual taxa with different levels of tolerance to environmental stressors. The sampling objective is to examine relative differences in assemblage composition between areas within the study area and outside of its potential influence using local and regional control sites. Metrics calculated may include:

• Richness-total number of unique taxa (many times with particular focus on the orders Ephemeroptera, Plecoptera, and Trichoptera).
• Sensitive taxa-total taxa from the orders Diptera, Ephemeroptera, Plecoptera, and Trichoptera.
• Sediment-sensitive taxa-total taxa from members of the orders Ephemeroptera, Plecoptera, and Trichoptera that qualify as "intolerant" or "sensitive."
• Hilsenhoff Biotic Index (HBI)-Index of organic pollution developed by Hilsenhoff (1988). Also known as community tolerance.
• Percent tolerant taxa-Proportion of individuals from taxa tolerant to disturbance.
• Percent sediment-tolerant taxa-Proportion of individuals from taxa tolerant to fine sediment.
• Percent dominant (single taxa)-Proportion of individuals from the single-most abundant taxon in the sample.

Based on a scoring system derived from these metrics, assessment of alterations in macroinvertebrates due to project effects on instream flows can be performed. As with the FFG approach, results are qualitative, and therefore may not have a strong nexus to specific project effects. Repeated sampling during alternate seasons and expert involvement is recommended to more accurately characterize the effect of instream flows on macroinvertebrate communities. This approach has been applied at the Carmen-Smith Hydroelectric Project (FERC Project No. 2242), on the McKenzie River, Oregon.

4.1.6.1 Selected references

Cummins, K. W., and M. J. Klug. 1979. Feeding ecology of stream invertebrates. Annual Review of Ecology and Systematics 10: 147-172.

Fore, L. S., J. R. Karr, and R. W. Wisseman. 1996. Assessing invertebrate responses to human activities: evaluating alternative approaches. Journal of the North American Benthological Society 15: 212-231.

Gislason, J. C. 1980. Effects of flow fluctuations due to hydroelectric peaking on benthic insects and periphyton of the Skagit River, Washington. Doctoral dissertation, University of Washington, Seattle.

Gislason, J. C. 1985. Aquatic insect abundance in a regulated stream under fluctuating and stable diel flow patterns. North American Journal of Fisheries Management 5: 39-46.

Gore, J. A., J. B. Layzer, and J. Mead. 2001. Macroinvertebrate instream flow studies after 20 years: a role in stream management and restoration. Regulated Rivers: Research and Management 17: 527-542.

Hilsenhoff, W. L. 1988. Rapid field assessment of organic pollution with a family-level biotic index. Journal of the North American Benthological Society 7: 65-68.

Karr, J. R. 1999. Defining and measuring river health. Freshwater Biology 41: 221-234

Karr, J. R., and E. W. Chu. 1997. Biological monitoring and assessment: using multi-metric indexes effectively. EPA 235-R97-001. University of Washington, Seattle.

Karr, J. R., and E. W. Chu. 1999. Restoring life in running waters: better biological monitoring. Island Press, Washington, D. C.

Merritt, R. W., and K. W. Cummins. 1996. An introduction to the aquatic insects of North America. Kendall/Hunt Publishing Company, Dubuque, Iowa.

Monk, W. A., P. J. Wood, D. M. Hannah, D. A. Wilson, C. A. Extence, and R. P. Chadd. 2006. Flow variability and macroinvertebrate community response within riverine systems. River Research and Applications 22: 595-615. doi:10.1002/rra.933.

Stillwater Sciences. 2006e. Aquatic habitats and instream flows at the Carmen-Smith Hydroelectric Project, upper McKenzie River basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon.

4.1.7 Freshwater mussel assessments

Freshwater unionid mussels (Mollusca, Bivalvia, Unionidae) are one of the most highly threatened and rapidly declining groups of freshwater organisms. They are sensitive to water quality conditions, and the presence of some species is considered an indicator of water quality. In addition, their life history traits (e.g. relatively immobile, long lifespan, filter-feeding, parasitic larval life stage on fish) make them susceptible to habitat disturbance and instream flow alterations in particular, since they cannot quickly adjust to flow fluctuations, or other regulations in instream flows. Because of their parasitic larval stage, they are also susceptible to habitat alterations affecting their host species.

Freshwater mussels appear to have specific habitat requirements, such as water depth and water velocity, similar to freshwater fish, and thus their suitability criteria can be considered during instream flows studies described above. However, their inability to react quickly to changes in flows complicates the procedures used to assess effects on other aquatic species. The following reference provides additional detail on an approach to evaluating the effects of hydroelectric project on freshwater mussels:

Layzer, J. B., and L. M. Madison. 1995. Microhabitat use by freshwater mussels and recommendations for determining their instream flow needs. Regulated Rivers: Research and Management 10: 329-345.

4.1.8 Comparison of regulated and unimpaired flows and temperature patterns

The timing of alterations to instream flows can have additional impacts on aquatic systems, beyond simply modifying the amount of habitat available. Many components of life history timing, such as migration cues, or breeding cycles, are affected by the timing of fluctuations in instream flows. A common approach to analyzing these effects is an office-based analysis to compare habitat and flow conditions under unimpaired and regulated flow scenarios. Differences in hydrographs of synthesized unimpaired vs. regulated flow can be analyzed for daily average flows for the entire water year, and also for the time periods that correspond to specific life stages (e.g., incubation, fry development, migration, spawning). As a result, temperature and flow data can be plotted to correspond to these life stages. This analysis of average daily flow and temperature fluctuations under synthesized unimpaired and regulated hydrology can be used to indicate higher and lower potential for impacts on life history events, such as stranding of fry, desiccation of incubating eggs, or migration cues.

4.1.9 Floodplain assessments

Extensive floodplains, often miles wide, are common in many rivers throughout the country, particularly in the Southeast. Approaches have been developed to assess the effects of flow alterations on floodplains and associated plant communities, including:

• Floodplain Inundation Method (Benke et al. 2000)
• Radar-based modeling (Townsend and Foster 2002).

Approaches to assessing the effects of instream flows on floodplains have been applied on the Ogeechee River, Georgia (Benke et al. 2000), and on the Catawba River, at the Catawba-Wateree Project (FERC Project No. 2232), North Carolina.

4.1.9.1 Selected references

Annear, T., I. Chisholm, H. Beecher, A. Locke, P. Aarrestad, N. Burkhart, C. Coomer, C. Estes, J. Hunt, R. Jacobson, G. Jobsis, J. Kauffman, J. Marshall, K. Mayes, C. Stalnaker, and R. Wentworth. 2004. Instream Flows for Riverine Resource Stewardship, revised edition. Instream Flow Council, Cheyenne, WY.

Benke, A. C., I. Chaubey, G. M. Ward, and E. L. Dunn. 2000. Flood pulse dynamics of an unregulated river floodplain in the southeastern U. S. coastal plain. Ecology 81: 2730-2741.

Townsend, P. A., and J. R. Foster. 2002. A synthetic aperture radar-based model to assess historical changes in lowland floodplain hydroperiod. Water Resources Research 38: 20.1-20.10.

4.1.10 Flow prescriptions

Instream flow studies typically focus on the effect of project-related alterations in instream flows on the availability of habitat for aquatic organisms. After these studies are conducted, relicensing participants are often tasked with developing flow prescriptions for the project area. Although the methods discussed above are primarily focused on establishing base flows, or the minimum required flows for a particular species and life stage, natural variability in flow regimes is also important to ecological integrity, as discussed in Poff et al. (1997). Other ecological functions of flows, such as lateral connectivity to riparian zones and floodplains, are crucial, as discussed in Annear et al. (2004). This report focuses on assessing project effects on instream flows, and does not attempt to compare approaches to developing flow prescriptions. However, four methods to determine flow prescriptions are briefly discussed below to provide a general overview, including a geomorphic approach, a population dynamics modeling approach, an environmental approach, and an approach using a combination of predictive models. In some cases, data collected during other relicensing studies are adequate to employ these approaches, but in other cases, flow prescriptions become a key element to a new license, and specific studies are necessary. Although the Tennant (1976) method (also known as the Montana method) is not discussed here, it is a hydraulic approach based on percentages of averages of annual flow.

Selected references

Anderson, K. E., A. J. Paul, E. McCauley, L. J. Jackson, J. R. Post, and R. M. Nisbet. 2006. Instream flow needs in streams and rivers: the importance of understanding ecological dynamics. Frontiers in Ecology and the Environment 4: 309-318.

Annear, T., I. Chisholm, H. Beecher, A. Locke, P. Aarrestad, N. Burkhart, C. Coomer, C. Estes, J. Hunt, R. Jacobson, G. Jobsis, J. Kauffman, J. Marshall, K. Mayes, C. Stalnaker, and R. Wentworth. 2004. Instream Flows for Riverine Resource Stewardship, revised edition. Instream Flow Council, Cheyenne, WY.

Poff, N. L., J. D. Allan, M. B. Bain, J. R. Karr, K. I. Prestergaard, B. D. Richter, R. E. Sparks, and J. C. Stromberg. 1997. The natural flow regime: a paradigm for river conservation and restoration. BioScience 47: 769-784.

Tennant, D. L. 1976. Instream flow regimens for fish, wildlife, recreation and related environmental resources. Pages 359-375 in J. F. Orsborn and C. H. Allman, editors. Instream flow needs. American Fisheries Society, Bethesda, Maryland.

4.2.1 Hydraulic modeling

The modeling approach to assessing fish stranding consists of collecting detailed three-dimensional data in areas believed to be sensitive to flow fluctuations (e.g., wide, shallow areas; backwater areas; tributary confluences; side-channel entrances; channel locations with geomorphically terraced features that tend to create isolated pools; etc.). Typically, data collected using a total station or light detection and ranging (LIDAR) are used to generate a topographic surface in a GIS data layer, similar to the methods described for modeling instream flows in Section 4.1.3. A one- or two-dimensional hydraulic model (e.g., HEC-RAS, PHABSIM) is then used to better understand the relationship between flow, water surface elevation (stage), and a given river feature that could pose a risk of stranding for aquatic organisms (Figure 8). Model results are then used to identify project operations, such as flow fluctuations at particular flow levels, that pose a high risk of causing stranding.

4.2.1.1 Advantages and disadvantages of approach

Use of hydraulic modeling to assess stranding has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• Multiple metrics can be evaluated, including rate of down ramping, area of inundation, and critical river stage.
• Modeling makes it possible to evaluate a range of flows, or project operations, including future operational modifications.
• Transects established for IFIM instream flow studies can also be used with PHABSIM to evaluate stranding risk.

Disadvantages

• Modeling is an assessment of risk, and does not determine the actual magnitude of stranding that will occur.
• The method is relatively intensive, and typically only small areas can be evaluated, unless river-wide data such as LIDAR are collected.

4.2.1.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• If LIDAR or other means are used to collect high-resolution bathymetric data, long reaches of rivers can be evaluated.
• Resolution and scale of the data collection and modeling results need to be considered, especially in low-gradient features, such as cobble bars.
• Modeling is appropriate in areas where future project operations may include changes in rates and magnitudes of fluctuations that cannot be evaluated under current conditions.
• Has been applied by the Grant County Public Utility District on the Hanford Reach of the Columbia River, Washington; in the lower Yakima River, Washington; and at the Bennetts Bridge and Lighthouse Hill developments on the Salmon River, New York.

4.2.1.3 Selected references

Milhous, R.T. 1998. A review of the physical habitat simulation system. In: Hydroecological Modelling: Research, practice, legislation, and decision-making. Praha, Czech Republic: T.G. Masaryk Water Research Institute. p. 7-8.

Prewitt, C. M., and C. Whitmus. 1986. A technique for quantifying effects of daily flow fluctuations on stranding of juvenile salmonids. Instream Flow Chronicle (Colorado State University Conference Services) 2: 1-3.

Tiffan, K. F., R. D. Garland, and D. W. Rondorf. 2002. Quantifying flow-dependent changes in subyearling fall chinook salmon rearing habitat using two-dimensional spatially explicit modeling. North American Journal of Fisheries Management 22: 713-726.

Whited, D., J. A. Stanford, and J. S. Kimball. 2002. Application of airborne multispectral digital imagery to quantify riverine habitats at different base flows. 18.

4.2.2 Direct observation

The direct observation, or empirical, approach to assessing stranding consists of direct observations to search for fish and/or invertebrates that have become isolated from the primary water body, or redds or egg masses that have become dewatered during periods when the water surface elevation is decreasing (i.e., down ramping and drawdown events). Surveys are typically focused in areas believed to be sensitive to flow fluctuations. Surveys are often conducted during down ramping and drawdown events caused by hydroelectric project operations during susceptible time periods for specific species and life stages. As flows recede during down ramping and drawdown events, biologists can conduct surveys from banks, or in-water snorkel surveys, or in-water electrofishing, in areas that are being dewatered and in vegetation and substrates. Transects can be established (Figure 9) for repeated surveys to increase the power of statistical analysis, and allow overall magnitude of stranding to be estimated.

4.2.2.1 Advantages and disadvantages of approach

Use of direct observation surveys to assess stranding has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• Allows direct observations of stranding events, including the species and life-stages potentially affected.
• Is compatible with study designs to estimate total magnitude of stranding.
• Ancillary information can be gained, such as lag times between operational changes and flow fluctuations, and the types of features or river stages most susceptible to stranding.

Disadvantages

• Accessibility to sites may be difficult in some systems.Potential for loss due to predation is difficult to quantify.
• In order to calculate annual mortality values, multiple observations are needed to account for differences in stranding potential due to seasonality, daily behavioral patterns, and project operations; it may be difficult to capture all of these differences.
• Can only be used to quantify stranding during the conditions that are observed, and predicting effects under alternate operations is difficult.
• There are limitations to the ability to observe stranded organisms, especially early life-stages of fish that preferentially select shallow habitat with cover. The error associated with observational accuracy is difficult to quantify, but can be estimated with separate trials.

4.2.2.3 Selected references

Nugent, J., T. Newsome, P. Hoffarth, M. Nugent, W. Brock, and Jr. M. Kuklinski. 2002. 2001 Evaluation of juvenile fall Chinook salmon stranding on the Hanford Reach of the Columbia River. BPA Contract Number 9701400, GCPUD Contracts Document 97BI30417. Prepared by Washington Department of Fish and Game for the Bonneville Power Administration, the Public Utility District Number 2 of Grant County.

USFWS (U. S. Fish and Wildlife Service). 2002. Trinity River juvenile fish stranding evaluation May-June, 2002. Report Number AFWO-F-01-03.

Stillwater Sciences. 2006. Flow fluctuations and stranding at the Carmen-Smith Hydroelectric Project, upper McKenzie River Basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon.

4.2.3 Experimental net enclosures

To experimentally evaluate the potential for fish stranding during water surface elevation fluctuations, field trials using fish placed in experimental enclosures can be conducted. For this approach, fish are enumerated, measured, and released into enclosures during periods of water surface elevation fluctuations in reservoirs or river reaches affected by project operations (Figure 10). Enclosures may have a live box to capture all fry that move toward the channel as flows recede. Repeated visual observations are used to continually monitor the effects of stranding on individuals during the experiment. Emigration, direct mortality, delayed mortality, and injury are recorded for each trial. Experiments may be repeated at different locations or periods to assist in accounting for variables such as rate and magnitude of water fluctuations, time of day, season, topography, substrate characteristics, water quality, and water temperature.

4.2.3.1 Advantages and disadvantages of approach

Use of experimental net enclosures to assess stranding has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• Specific geomorphic features and project operations can be evaluated in separate trials.
• Species- and life-stage-specific trials can be conducted.
• Fish behavior and delayed effects of flow fluctuations on fish can be evaluated.
• Statistically robust, since the number of fish that are susceptible to stranding is known, and probability of detection is high.

Disadvantages

• Fish used for the experiment (typically from hatcheries) may not adequately simulate species composition, behaviors, and abundance in the system.
• Nets are difficult to deploy, and therefore typically only a few sites are evaluated. Results from the experiment may be difficult to extrapolate spatially and temporally.
• If multiple replicates are conducted to increase statistical robustness, other environmental factors such as weather and water temperature and quality affect results. In addition, it may not be possible to reproduce water surface fluctuations of the same rate and magnitude, which may also affect results.

4.2.3.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• In systems where few fish are expected to be stranded, this approach can account for detection probability, since a known number of fish are used.
• This approach works well if areas with a potential for stranding are homogeneous, such that results from focused test in one area can be applied to other areas.
• Has been applied at the Bratsberg power station, on the Nidelva River, Norway.

4.2.3.3 Selected references

Bradford, M. J. 1997. An experimental study of stranding of juvenile salmonids on gravel bars and in sidechannels during rapid flow decreases. Regulated Rivers 13: 395-401.

Bradford, M. J., G. C. Taylor, J. A. Allan, and P. S. Higgins. 1995. An experimental study of the stranding of juvenile coho salmon and rainbow trout during rapid flow decreases under winter conditions. North American Journal of Fisheries Management 15: 473-479.

Halleraker, J.H., Saltveit, S. J., Harby, A., Arnekleiv, J.V., Fjeldstad, H.P. and Kohler, B. 2003. Factors influencing stranding of wild juvenile brown trout (Salmo trutta) during rapid and frequent flow decreases in an artificial stream. Journal of Rivers Research and Application 19: 589-603.

Saltveit, S. J., J. H. Halleraker, J. V. Arnekleiv, and A. Harby. 2001. Field experiments on stranding in juvenile Atlantic salmon (Salmo salar) and brown trout (Salmo trutta) during rapid flow decreases caused by hydropeaking. Regulated Rivers: Research and Management 17: 609-622.

4.2.4 Macroinvertebrate assessments

Flow fluctuations generated from ramping at hydroelectric facilities for operational, recreational, or even "environmental" (e.g. channel maintenance, or smolt outmigration) purposes can cause increased velocities and shear stress, bedload mobilization, and scour, all of which can contribute to decreases in species abundance, richness, and diversity. Decreases in invertebrate community measures can result from the initial physical disturbance causing increased macroinvertebrate drift, but can also result from changes in the community structure caused by response to chronic flow fluctuations. Over time, species that are more vulnerable to stranding and desiccation from lateral water surface changes or those more susceptible to entrainment during increased flows may be replaced by more tolerant species, thus altering community indices. As described in Section 4.1.6, the FFG and IBI approaches can be used to provide information on the effect of altered instream flows (which includes flow fluctuations) on benthic macroinvertebrate communities. In addition to these methods, drift monitoring techniques can be employed to study the effects of flow fluctuations from ramping at hydroelectric projects.

4.2.4.1 Selected references

Brittain, J. E., and T. J. Eickeland. 1988. Invertebrate drift-a review. Hydrobiologia 166: 77-93.

Cortes, R. M. V., M. T. Ferreira, S. V. Oliveira, and D. Oliveira. 2002. Macroinvertebrate community structure in a regulated river segment with different flow conditions. River Research and Applications 18: 367-382.

Gislason, J. C. 1980. Effects of flow fluctuations due to hydroelectric peaking on benthic insects and periphyton of the Skagit River, Washington. Doctoral dissertation, University of Washington, Seattle.

Gislason, J. C. 1985. Aquatic insect abundance in a regulated stream under fluctuating and stable diel flow patterns. North American Journal of Fisheries Management 5: 39-46.

Leibfried, W. C., and D. W. Blinn. 1987. Effects of steady versus fluctuating flows on aquatic macroinvertebrates in the Colorado River below Glen Canyon Dam, Arizona. Final report. Arizona Game and Fish Department Contract 6400042. National Technical Information Service, Springfield, Virginia.

R2 Resource Consultants. 2005. Effects of pulse type flows on benthic macroinvertebrates and fish: a review and synthesis of information. Prepared by RD Resource Consultants, Inc., Redmond, Washington and Pacific Gas & Electric Company, San Ramon, California.

Troelstrup, N. H., Jr., and G. L. Hergenrader. 1990. Effect of hydropower peaking flow fluctuations on community structure and feeding guilds of invertebrates colonizing artificial substrates in a large impounded river. Hydrobiologia 199: 217-228.

4.3.1 Introduction

For certain fish populations residing in the vicinity of hydroelectric projects, a major source of direct and indirect mortality is the physical damage or stress individuals incur as they attempt downstream passage through hydropower facilities (Figure 1 shows typical facilities). Migratory fish species, such as salmon and lamprey, are especially affected because they may need to migrate downstream to successfully complete their life cycle. The phenomenon of fish being drawn into physical features of hydropower facilities is termed “entrainment.” Entrainment is generally considered to be the movement of fish from a reservoir through various water conveyances at each dam to downstream exit locations, which can result in injury, mortality, and delay of downstream migrants. Entrainment effects can occur at various project facilities, including spillways, turbines, fish ladders, and downstream fish bypass facilities.

Several approaches for evaluating entrainment rates and impacts on downstream migrants at project facilities are used by researchers, the most common of which are discussed below, including hydroacoustics, individual tagging techniques, experimental releases of fish, sensor fish devices, and direct capture or trapping. In addition to these field-based approaches, modeling is also used. The modeling approach (which is not evaluated in detail here) uses available data from empirical studies (on site or from other facilities), data on the specifics of the facility (e.g., turbine characteristics, head, flow, available routes) and then employs a numerical model for predicting turbine or spillway passage survival. In many applications, the basis for the predicted survival estimates is a model developed by Franke et al. (1997), which was developed as part of the Department of Energy Advanced Hydro Turbine System program begun in the 1990s. In some cases, numerical modeling is used as a substitute for the field-based approaches described below. The following link provides several references on all of the approaches discussed here, including numerical modeling and other approaches for evaluating entrainment effects of turbines and spillways at hydroelectric facilities.

4.3.1.1 Selected Reference

Franke, G. F., D. R. Webb, Jr. R. K. Fisher, D. Mathur, P. N. Hopping, P. A. March, M. R. Headrick, I. T. Laczo, Y. Ventikos, and F. Sotiropoulos. 1997. Development of environmentally advanced hydropower turbine system design concepts. Office Contract DE-AC07-94ID13223. Prepared for U. S. Department of Energy, Idaho Operations Office, and Hydropower Research Foundation, Inc.

4.3.2 Hydroacoustics

Fish movements can be tracked using hydroacoustic transducers. The transducers are placed near turbine intakes, or spillways, to detect the movement of fish through various downstream passage routes. Hydroacoustic transducers record echoes from objects passing through an acoustic beam. Mean target strengths of echo traces can be categorized into fish-equivalent length classes to interpret detected objects consistent with the fish species and life stages for a particular study area. The use of fish-equivalent length classes provides more information on the life-stages of fish entrained than pooled estimates for all length classes. Hydroacoustic estimates represent a relative index of entrainment rather than an absolute estimate because of false detections from debris, and the necessity of data filtering. The relative index allows many comparisons, including comparisons of various project operations, seasonal trends, daily trends, different life-stages, and various passage routes.

Although not discussed in detail here, the Pacific Northwest National Laboratory (PNNL) has been working with an alternative approach to hydroacoustics called an acoustic camera. Using Dual-frequency Identification Sonar (DIDSON), which was originally developed by the United States Navy's Space and Naval Warfare Systems Center, the acoustic camera promises to provide high resolution imaging of fish in turbid and low-light conditions. This technology is beginning to be experimentally deployed at some Columbia River projects.

4.3.2.1 Advantages and disadvantages of approach

Use of hydroacoustics to measure entrainment has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages:

• Estimates of fish size are provided.
• Accuracy of detections are not light-sensitive.
• The equipment can be used in deep water locations.
• Estimates for individual passage routes can be provided, including seasonal and diel variation.
• Does not have to rely on a potentially biased sub-sample of fish, and instead evaluates any fish that passes detector.
• Has the ability to provide a continuous record at multiple passage routes simultaneously, so temporal and spatial patterns can be evaluated relative to project operations.

Disadvantages:

• The same fish may be detected more than once.
• Debris and bubbles in the water may be falsely counted as detections.
• Data filters used to eliminate false detections may eliminate actual detections.
• Reverberation noise and poor resolution near the substrate makes shallow water sampling difficult.
• Samples only a portion (typically 5–50%) of the intake, therefore extrapolation is necessary.
• Can only provide a relative index to fish passage unless calibrated by net sampling, and cannot directly provide species-specific estimates.

4.3.2.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• Will always provide more reliable results when detections are verified with direct captures or observations.
• May not be the best option for shallow water.
• Should not be used in a system that passes relatively high amounts of debris.
• Site-specific constraints on the placement of transducers include excessive turbulence, solid boundary layers, underwater obstructions, debris levels, and level fluctuations.
• Can be applied to facilities with numerous intakes.
• False detections can be recorded at units that frequently turn off and on if fish swim into units that are off-line. Records of project operations that indicate when routes are available are required for accurate evaluations.
• Has been applied at numerous large dams on the Columbia and Snake rivers, including at the Bonneville Hydroelectric Project (owned by the USACE, Portland District). Has also been applied at small dams, including at the Carmen-Smith Hydroelectric Project (FERC Project No. 2242), on the McKenzie River, Oregon.

4.3.2.3 Selected references

Ecology Group. n.d. Fisheries hydroacoustic technologies. Ecology Technical Group, Environmental Technology Division, Pacific Northwest National Laboratory, Richland, Washington.

EPRI (Electric Power Research Institute). 1992. Fish entrainment and turbine mortality review and guidelines. Final Report. Research Project 2694-01; EPRI TR-101231. Palo Alto, California.

Hedgepeth, J.B., D. F. Fuhriman, G. M. W. Cronkite, Y. Xie, and T. J. Mulligan. 2000. Atracking transducer for following fish movement in shallow water and at close range. Aquat.
Living Resour., Vol 13, 305-311.

Johnson, G. E., J. R. Skalski, and D. J. Degan. 1994. Statistical precision of hydroacoustic sampling of fish entrainment at hydroelectric facilities. North American Journal of Fisheries Management 14: 323-333.

Johnson, R. L., S. M. Anglea, S. L. Blanton, M. A. Simmons, R. A. Moursund, G. E. Johnson, E. A. Kudera, J. Thomas, and J. R. Skalski. 1999. Hydroacoustic evaluation of fish passage and behavior at Lower Granite Dam in spring 1998. Final report, PNWD-2448. Prepared by Battelle, Pacific Northwest Division, Richland, Washington for U. S. Army Corps of Engineers, Walla Walla District, Walla Walla, Washington.

Ploskey, G. R., C. R. Schilt, J. Kim, C. W. Escher, and J. R. Skalski. 2003. Hydroacoustic evaluation of fish passage through Bonneville Dam in 2002. Final report PNNL-14356. Prepared by Pacific Northwest National Laboratory, Richland, Washington for U. S. Army Corps of Engineers, Portland, Oregon.

4.3.3 Individual tagging

Entrainment rates and behavioral patterns of fish can be detected using individual transmitting tags (e.g., radio and acoustic) (Figure 11) or transponding tags (e.g., passive integrated transponder [PIT]) (Figure 12). Transponding tags require an external energy source to activate the tag for data retrieval, and are able to provide information on rate of entrainment and passage route selection. Transmitting tags operate by sending either pulsed or coded signals that can be detected with tracking devices, and are also able to provide information on specific behaviors such as delay and structure avoidance in addition to rate of entrainment and passage route taken. The following reference provides a detailed comparison of various tagging methods:

Nielsen, L. A., and D. L. Johnson. 1983. Fisheries techniques. American Fisheries Society, Bethesda, Maryland.

4.3.3.1 Advantages and disadvantages of approach

Use of individual tags to measure entrainment has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• PIT tags are not dependent on batteries, and can remain inert inside a fish for the duration of its life.
• PIT tags are small (typically 11–28 mm in length and 2.1–3.5 mm in diameter), and can thus be used on juvenile fish.
• PIT tags are relatively inexpensive, and can provide a large sample size.
• Transmitting tags have a relatively large detection range (generally > 1 km).
• Transmitting tags can be used to study impingement rates.
• Transmitting tags can be used at sites where fish recovery is difficult.
• Transmitting tags can provide precise data on the behavior of individual fish, and is not limited by waiting for fish to pass detectors.
• Often multiple evaluations can be conducted from one group of tagged fish, including travel time, movement trajectories, forebay residency time, survival, and habitat use.
• When there are multiple passage routes, it can be determined which route fish used.
• Precision of data is conducive to statistical analysis.

Disadvantages

• PIT-tags have a very limited detection range (approximately 20 cm).
• Transmitting tags are large, expensive, and require extensive handling of fish, thus often limiting sample size. Often only a sub-sample of the population can effectively be tagged, potentially biasing results.
• Transmitting tags are relatively large, and cannot be used on small or juvenile fish.
• Sampling duration using transmitting tags is limited by the battery life.
• In some cases, handling and tagging of fish leads to aberrant behavior.
• Data obtained for tagged fish may not apply to untagged fish.

4.3.3.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• Tag type will be dictated by fish size and species, type of data to be collected, habitat utilization, and structure characteristics.
• Acoustic tag detections can be affected by thermal stratification, vegetation, boat noise, and high levels of suspended sediment, and turbulence.
• Radio tags become less effective when fish utilize shallow habitats >5 m deep, or when water conductivity is high.
• In systems with multiple species of interest, often only a few species can be effectively tagged and monitored. However, all tagged individuals provide species-specific data.
• When multiple passage routes are available, the small sample sizes can become highly partitioned, decreasing the power of the analysis.
• Has been applied at numerous hydropower projects on the Columbia River, including the Bonneville Hydroelectric Project (owned by the USACE, Portland District) and the Dalles Hydroelectric Project (FERC Project No. 7076); and at the Upper Skagit River Hydroelectric Project (FERC Project No. 553), on the Skagit River, Washington; and at the Alabama Power Company Coosa River and Warrior River Hydroelectric Projects (FERC Project Nos. 2146, 2165), on the Coosa and Warrior rivers.

4.3.3.3 Selected references

EPRI (Electric Power Research Institute). 1992. Fish entrainment and turbine mortality review and guidelines. Final Report. Research Project 2694-01; EPRI TR-101231. Palo Alto, California.

Ploskey, G. R., C. R. Schilt, J. Kim, C. W. Escher, and J. R. Skalski. 2003. Hydroacoustic evaluation of fish passage through Bonneville Dam in 2002. Final report PNNL-14356. Prepared by Pacific Northwest National Laboratory, Richland, Washington for U. S. Army Corps of Engineers, Portland, Oregon.Hedgepeth, J., D. Fuhriman and W. Acker. 1999. Fish behavior measured by a tracking radar-type acoustic transducer near hydroelectric dams. Pages 155–171 in M. Odeh, editor. Innovations in fish passage technology. American Fisheries Society, Bethesda, Maryland.

MacLennan, D. N., and E. J. Simmonds. 1992. Fisheries acoustics. Chapman and Hall, London.

Hedgepeth, J. B., D. Fuhriman, G. M. W. Cronkite, Y. Xie, and T. J. Mulligan. 2000. A tracking transducer for following fish movement in shallow water and at close range. Aquatic Living Resources 13: doi:10.1016/S0990-7440(00)01089-5.
Kleinschmidt Associates. 2002. Alabama Power Company Coosa and Warrior River projects. E11 - impingement, entrainment, and turbine mortality study progress report III. Draft report. Prepared by Kleinschmidt Associates Energy and Water Resource Consultants.

Voegeli, F. A., and D. G. Pincock. 1996. Overview of underwater acoustics as it applies to telemetry. E. Baras and J. C. Philippart, editor. Underwater Biotelemetry.

4.3.4 Experimental release of batch-marked fish

Injury and mortality rates through a specified structure can be determined by experimentally releasing a batch of fish through a given structure and then recovering these fish at the outlet of the structure. Experimental fish may be released either with or without a tag; however, tags such as balloon and transponding tags (e.g., radio and acoustic) will increase the probability for recovery. The HI-Z Turb’N Tag is a “balloon tag” consisting of small deflated plastic balloons that are externally mounted to test fish (Figure 13). After the fish are released, the balloons will inflate after a predetermined time period, which will bring the fish to the surface where they can be recaptured. Other types of batch marks (e.g. fin-clips, dye, inkjet, or coded wire tags) are also useful for denoting individuals for test releases, although they do not allow as precise of an analysis as individual tags.

4.3.4.1 Advantages and disadvantages of approach

Use of experimental releases of fish to measure entrainment has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• Balloon tags can be used on fish that are sensitive to handling.
• Assessment of delayed mortality is possible.
• Ability to recapture nearly all fish released provides a statistically rigorous estimate of entrainment mortality and injury rate.
• Multiple trials using different passage routes, species, size classes, and project operations can be used to test differences in injury and mortality rates.

Disadvantages

• Testing wild fish is often not possible, limiting analysis to surrogates, usually hatchery fish.
• Sample sizes required for adequate statistics may limit the number of trails conducted.

4.3.4.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• Recovery of fish may be difficult in tailraces where boat access is limited or unsafe.
• Has been applied at numerous dams on the Columbia River, including the Bonneville Hydroelectric Project (owned by the USACE, Portland District) and the Dalles Hydroelectric Project (FERC Project No. 7076); and at the Willamette Hydroelectric Project (FERC Project No. 2233) on the Willamette River.

4.3.4.3 Selected references

EPRI (Electric Power Research Institute). 1992. Fish entrainment and turbine mortality review and guidelines. Final Report. Research Project 2694-01; EPRI TR-101231. Palo Alto, California.

Ferguson, J. W., G. M. Matthews, R. L. McComas, R. F. Absolon, D. A. Brege, M. H. Gessel, and L. G. Gilbreath. 2004. Passage of adult and juvenile salmon through federal Columbia River power system dams. NOAA Technical Memorandum. NOAA Fisheries, Fish Ecology Division, Fish Ecology Division, Northwest Fisheries Science Center.

Normandeau Associates. 2001. Fall 2000 evaluation of juvenile spring chinook salmon downstream migration at the Willamette Falls Project under two passage scenarios. Final Report. Prepared for Portland General Electric Company, Portland, Oregon, Blue Heron Paper Company, Oregon City, Oregon, and Willamette Falls Project Fisheries, Aquatics, and Terrestrial Workgroup.

Normandeau Associates. 2001. Feasibility of estimating direct mortality and injury on juvenile salmonids passing the Dalles Dam Spillway during high discharge. Contract No. DACW68-96-D-0003, Task Order DT04.

Normandeau Associates, Inc., J. R. Skalski, and Mid Columbia Consulting, Inc. 1996.Potential effects of spillway flow deflectors on fish condition and survival at the
Bonneville Dam, Columbia River. Report to U.S. Army Corps of Engineers, Portland District, Portland, Oregon.

4.3.5 Sensor fish device

Sensor fish are artificial devices containing microsensor transducers to measure the three types of forces (tensile force, compression, and shear strain) a fish may experience during passage. Sensor fish approximate the size and shape of actual fish, and were originally designed as a smolt-sized salmonid surrogate (Figure 14). When released through a passage route and then recovered downstream, sensor fish can provide information on the types of conditions and mechanism that result in various types of injuries.

4.3.5.1 Advantages and disadvantages of approach

Use of the sensor fish devise to assess entrainment effects has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• This method is able to provide substantial information on the source of injury, which can be used to make recommendations on project improvements for passage efficiency.
• Live fish do not have to be used.
• Sensor fish can easily be retrieved by attaching microtransmitters or balloon tags.
• Assessment of multiple passage routes and project operations is possible.

Disadvantages

• Currently sensor devices are too large to be placed inside live fish, and the artificial sensor fish does not simulate behavior of live fish.

4.3.5.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• This approach is best used when entrainment and mortality rates are either known or not relevant. The sensor fish can determine appropriate measures for modifying project facilities to lower impacts, but does not determine the rate of those impacts.
• Has been applied at numerous dams on the Columbia River; at the Lower Granite Hydroelectric Project and at the Ice Harbor Hydroelectric Project (both owned by the USACE, Walla Walla District) on the Snake River, Washington; and at the Prosser Irrigation District Dam on the Yakima River, Washington.

4.3.5.3 Selected references

Janowski, P. 2000. Running the dam gauntlet: in the name of science, a rubber fish serves as stunt double. Scientific American March: 18.

Carlson, T. J., J. P. Duncan, and T. L. Gilbride. 2003. The sensor fish: measuring fish passage in severe hydraulic conditions. Hydro Review 22 (6): 62-69.

Carlson, T. J., and J. P. Duncan. 2004. Characterization of spillway passage conditions at Ice Harbor Dam, Snake River, Washington, 2003. Draft final report PNWD-3462. Prepared by Battelle, Pacific Northwest Division, Richland, Washington for U. S. Army Corps of Engineers, Walla Walla, Washington.

Johnson, R. L., B. G. Gray, S. L. Blanton, J. P. Duncan, R. W. Gilbert, G. A. Anderson, and D. A. Neitzel. 1998. Advanced Sensor Tag for Improved Turbine Design. Pacific Northwest National Laboratory, Internal Report, Richland Washington.

4.3.6 Direct capture or trapping

The direct capture or trapping approaches to evaluating entrainment consist of using standard traps such as rotary screw traps or fyke traps to capture fish exiting a spillway or turbine (Figure 15). Fish captured provide an indication of the rate and impacts of entrainment.

4.3.6.1 Advantages and disadvantages of approach

Directly capturing or trapping fish to measure entrainment has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• Some traps are capable of sampling all of the intake area.
• Accounts for natural fish behavior since the “test” fish occur naturally.
• Potential for large sample sizes if many fish are being entrained.
• Delayed effects can be monitored.
• Continuous data can be provided.
• Provides other relevant information, such as species composition, migration timing, or size at downstream migration.
• Provides indisputable evidence of entrainment impacts.

Disadvantages

• Access to collection equipment may be difficult.
• Project operations (such as sudden high-volume releases) and debris loading may dislodge or damage collection equipment.
• The cause of injury or mortality may be ambiguous (e.g., if an injury is detected, it may be unknown if it is caused by passage, the collection equipment, or predation inside the collection equipment).
• The equipment used to collect fish may injure or kill the fish.
• Because it is labor-intensive and can injure or kill fish, it is rarely used continuously, so temporal or spatial trends are rarely evaluated.
• This method is not generally statistically robust (especially in large systems), though evaluation of trap efficiencies can improve estimates.
• The timing of entrainment may be unknown.
• The route used for passage may be unknown.

4.3.6.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• Sampling feasibility and placement of collection units may be dictated by project characteristics, and collection units may need to be placed in sites that are not most desirable for sampling.
• In a large system with large volumes of water to sample, this method does not work well. This method does work well in smaller systems when all or most of the water volume can be sampled. Volume of water, and the proportion of the area sampled will affect the trapping efficiency, and consequently the statistical power of the direct capture method.
• Has been applied at numerous dams on the Columbia River, including at the John Day Hydroelectric Project (owned by the USACE, Portland District); at the Tower and Kleber Hydroelectric Project (FERC Project No. 10615) on the Black River, Michigan; and at the Cougar Hydroelectric Project Dam (owned by the USACE, Portland District) on the South Fork McKenzie River, Oregon.

4.3.6.3 Selected references

Johnston, S. V., B. H. Ransom, and J. R. Bohr. 1993. Comparison of hydroacoustic and net catch estimates of fish entrainment at Tower and Kleber Dams, Black River, Michigan. Waterpower Conference Proceeding Paper 1: 308-317.

Ploskey, G. R., and T. J. Carlson. 1999. Comparison of hydroacoustic and net estimates of fish guidance efficiency of an extended submersible bar screen at John Day Dam. North American Journal of Fisheries Management 19: 1066-1079.

4.4.1 Radio tagging

The radio tagging approach to assessing effects on upstream passage consists of capturing upstream-migrating fish (usually adult life-stage) and inserting radio tags (Figure 12). Often a series of continuous data-logging radio receivers are installed at key locations in the project vicinity to monitoring entry into and exit from specific areas, including velocity barriers, fish ladders, draft tubes, and tailraces. In addition, manual tracking is often conducted using boats, helicopters, vehicles, or on foot. Analysis consists of determining where fish occur, and how long fish are delayed in particular areas. This approach does not address direct effects on fish, such as turbine strike, unless fish are recaptured at the end of the study.

4.4.1.1 Advantages and disadvantages of approach

Use of radio tagging to assess upstream migration impacts at draft tubes has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• Radio tags have a relatively large detection range (generally > 1 km).
• Individual fish and their behaviors can be tracked, and the precision of data is conducive to statistical analysis. For example, small delays in migration of less than 24 hours can be detected, which could be significant to some populations (e.g. spawning salmon).
• Basic patterns in fish movements and areas used can be quickly ascertained.
• Continuous data collection allows relationships between fish behavior and project operations to be evaluated, and is helpful in designing potential modifications.
• Often multiple evaluations can be conducted from one group of tagged fish, including travel time, movement trajectories, forebay residency time, survival, and habitat use.

Disadvantages

• Transmitting tags are large, expensive, and require extensive handling of fish, thus often limiting sample size. Often only a sub-sample of the population can effectively be tagged, potentially biasing results.
• In some cases, handling and tagging of fish leads to aberrant behavior, including delay, which makes the results difficult to interpret.
• Sampling duration is limited by the battery life.
• Data obtained for tagged fish may not apply to untagged fish.

4.4.1.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• Radio tagging is an effective approach in many types of environments and facilities. If observations of multiple species are desired, the ability of one species to be a surrogate for others should be considered.
• Has been applied at many projects, including the Jackson Hydroelectric Project (FERC Project No. 2157), on the Sultan River, Washington; the Willamette Falls Hydroelectric Project (FERC Project No. 2233), on the Willamette River, Oregon; at the Seton Creek Hydroelectric Project, on Seton Creek, British Columbia; and at the Leaburg-Walterville Hydroelectric Project (FERC Project No. 2496), on the McKenzie River, Oregon.

4.4.1.3 Selected references

Brush, T. D., and D. Domina. 2001. Assessment of adult spring chinook salmon upstream passage and residency near T. W. Sullivan draft tubes. Draft report. Prepared by Normandeau Associates for Portland General Electric (PGE), Portland, Oregon, Blue Heron Paper Company, Oregon City, Oregon and Willamette Falls Project Fisheries, Aquatics, and Terrestrial Workgroup.

EA Engineering, Science, and Technology. 1991. Radio-tracking studies of adult spring Chinook salmon migration behavior in the McKenzie River, Oregon. Prepared for Eugene Water & Electric Board, Eugene, Oregon.

International Pacific Salmon Fisheries Commission. 1976. Tailrace delay and loss of adult sockeye salmon at Seton Creek Hydroelectric Plant. New Westminster, British Columbia, Canada.

Parametrix, Inc. 1985. Adult fish passage (Powerhouse Berm) study, Henry M. Jackson (Sultan River) Hydroelectric Project, FERC 2157. Snohomish County Public Utility District, No. 1.

4.4.2 Underwater observations

The direct observation approach to evaluating upstream passage effects typically consists of conducting snorkel and/or video surveys in the vicinity of draft tubes or other project features over a range of project operations. Surveyors record the number, species, and location of all fish observed, and document any sign of injuries (or mortalities).

4.4.2.1 Advantages and disadvantages of approach

Use of underwater observation assess upstream migration impacts at draft tubes has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• Sample sizes are typically high, since all fish observed can be recorded.
• Injuries and mortalities can be directly observed and documented.
• The relative number of fish that are delayed, or are in the vicinity of project facilities, can be estimated.

Disadvantages

• It is often not safe to sample in tailraces, or near draft tubes while they are operating.
• Because the survey is snapshot in time, it is often difficult to quantify periods of delay, or to examine all potential project operations.
• It can be difficult to distinguish between project-induced “delay”, and fish behaviors such as holding prior to a spawning migration, or using the tailrace as a feeding site, which may not be deleterious.

4.4.2.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• For visual observation surveys to be successful, water clarity has to be high enough to observe injuries on fish, and to observe dead fish that may be lying on the substrate.
• Has been applied at numerous projects, including the Winchester Dam (owned by the Winchester Water Control District) on the North Umpqua River, Oregon; and the Carmen-Smith Hydroelectric Project (FERC Project No. 2242) on McKenzie River, Oregon.

4.4.2.3 Selected references

Stillwater Sciences. 2006. Fish entrainment at the Carmen-Smith Hydroelectric Project, upper McKenzie River basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon.

William, R. 1985. Report on the loss of salmonid fish at the Winchester Hydroelectric Project in 1984, 11. Draft report. Oregon Department of Fish and Wildlife, Research and Development Station.

4.5.1 Genetic analysis

Over the last 10 years, molecular tools have been used to non-lethally characterize potential genetic problems in fish populations (e.g. inbreeding, hybridization, genetic drift, reduced genetic diversity, etc). Typically a small tissue sample is collected from an individual, preserved, and analyzed in a genetics laboratory. An investigation of population genetics using biochemical techniques can provide important information for assessment of project effects on habitat connectivity. The general categories of genetic investigation include population structure, life history diversity, genetic diversity, and population viability. The field of genetic analysis is rapidly evolving and many different types of testing are available (e.g., electrophoresis, polymerase chain reaction [PCR] analysis). Selecting the appropriate test for the specific questions involved is crucial. Because of the technological expertise required in selecting and performing the appropriate analysis, experts are typically involved in relicensing studies involving genetic analysis.

4.5.1.1 Advantages and disadvantages of approach

Use of genetic analysis to assess effects to aquatic habitat connectivity has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• Although fish are handled, only a small, non-lethal tissue sample is required.
• Direct way to measure the presumed effect.
• Many associated questions can be answered (e.g., can assess effects of introduced species hybridization with same analysis).

Disadvantages

• Large sample size with appropriate spatial consideration needed.
• Natural versus project-induced genetic trends may be difficult to discern.
• Can be difficult to discern how much genetic drift results in a significant threat to population viability.

4.5.1.2 Site-specific considerations and applicability

• Genetic analysis works equally well at all sites. If genetic data already exist for a population, it can make analysis more robust.
• Has been applied in river systems throughout the world.

4.5.1.3 Selected references

Allendorf, F. W., R. F. Leary, P. Spruell, and J. K. Wenburg. 2001. The problems with hybrids: setting conservation guidelines. Trends in Ecology and Evolution 16: 613-622.

Epifanio, J., G. Haas, K. Pratt, B. Rieman, P. Spruell, C. Stockwell, F. Utter, and W. Young. 2003. Integrating conservation genetic considerations into conservation planning: a case study of bull trout in the Lake Pend Oreille--lower Clark Fork River system. Fisheries 28: 10-24.

Neraas, L. P., and P. Spruell. 2001. Fragmentation of river systems: the genetic effects of dams on bull trout (Salvelinus confluentus) in the Clark Fork River system. Molecular Ecology 10: 1153-1164.

ODFW (Oregon Department of Fish and Wildlife). 2006. Native fish investigations project: publications. ODFW, Corvallis Research Lab, Corvallis, Oregon.

4.5.2 Spatial analysis

The use of spatial analysis to evaluate effects of projects on habitat connectivity typically consists of overlaying GIS coverages showing current and historical obstacles and barriers with coverages showing road networks, streams and reservoirs, as well as fish distribution in the study area. Results from this analysis can provide:

1. a comparison of the current and potential distribution of analysis species,
2. an assessment of potential seasonal limitations to movement, and
3. identification of potential sites for field reconnaissance or more detailed surveys.

There are standard methods for evaluating passage at barriers or culverts when spatial analysis identifies these sites, including:

Mirati, A. 1999. Assessment of Road Culverts for Fish Passage Problems on State-and County-Owned Roads. Statewide Summary Report Oregon Department of Fish and Wildlife.
National Marine Fisheries Service. 2001. Guidelines for salmonid passage at stream crossings. NMFS, southwest region.

In addition, radio tags and/or PIT tags can also be used to evaluate specific barriers, using similar approaches to those described in Section 4.3.3 and Section 4.4.1.

4.5.2.1 Advantages and disadvantages of approach

Use of spatial analysis to assess effects to aquatic habitat connectivity has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantage

• Quickly evaluate the magnitude of habitat connectivity effects over a broad spatial area, and prioritize areas for additional surveys.

Disadvantage

• Rarely provides complete analysis, and follow-up surveys typically are used.

4.5.2.2 Site-specific considerations and applicability

Many of the advantages and disadvantages of this approach will depend on site-specific considerations, as discussed below:

• Level of detail is adequate for large-scale disruptions to habitat connectivity, such as a dam. For final resolution, such as road crossings, this approach is a first step in screening and prioritizing sites, and follow-up surveys are typically required.
• Has been applied at numerous projects, including the North Umpqua Hydroelectric Project (FERC Project No. 1927), on the North Umpqua River, Oregon. In addition, the River Alliance applied a GIS-based assessment of dams in the Great Lakes basins, and in the Chippewa River basins.

4.5.2.3 Selected references

River Alliance of Wisconsin GIS-based analysis >>

Stillwater Sciences. 1998. Aquatic and riparian habitat connectivity. Pages 3-1 to 3-56 in The North Umpqua cooperative watershed analysis synthesis report. Prepared by Stillwater Sciences, Berkeley, California for PacifiCorp, Portland, Oregon.

4.6.1 Introduction

Hydroelectric projects potentially affect fish species in both detrimental and beneficial ways at different life-stages, and at varying spatial scales. Often these effects can be cumulative. For example, a project may reduce instream flows in a riverine reach, thus decreasing spawning and fry rearing habitat for fish, while providing increased adult foraging habitat in a reservoir, blocking a historical migration route at a dam, and providing increased access to a tributary by inundating a historical barrier. Population dynamic models have been developed to assess the multitude of potential project effects on the varying temporal and spatial patterns of the abundance of a species (Figure 16). The objectives of population modeling may include:

1. identifying factors most likely to affect the abundance of adults, the population’s age and size structure, and the population’s resilience to disturbance;
2. identifying potential threats that could lead to severe population decline or extirpation; and
3. evaluating project effects and the effectiveness of management options designed to maintain or increase the health of the populations by predicting relative changes in population size between various management options.

Many types of data are needed to evaluate population dynamics in study area, including fish distribution, population estimates, survival, growth, life history timing, and habitat availability. There are many methods available to collect each of these types of data, including PIT tag tracking, direct snorkel surveys, outmigrant trapping, spawning surveys, etc. Typically, data from all other studies conducted on a fish population would be used, including the habitat connectivity, entrainment, stranding, and instream flows studies previously discussed. Standard approaches to determine fish distribution, population estimates, survival, life-history, and growth are not discussed here, but these methods are fairly standard, and discussed in detail in Nielsen and Johnson (1983).

Conceptual or quantitative models can be developed for a population. The conceptual models provide a theoretical foundation for the quantitative models by identifying factors that limit life history stages, and factors that limit the overall production of the populations. Quantitative models can provide a framework for investigating the relative influences of various factors on each life-stage.

Although many models have been developed to evaluate fish populations, four approaches that are currently being used at hydroelectric projects are discussed below as examples of the modeling approach. Additional models include:

• Coastal Landscape Analysis and Modeling Study (CLAMS)
• The Electric Power Research Institute program on compensatory mechanisms in fish populations (EPRI CompMech)
• Qualitative Habitat Assessment (QHA)
• Salmonid Watershed Analysis Model (SWAM)
• Cumulative Risk Initiative (CRI)
• Salmon Habitat & Recovery Planning (SHRP)
• Umpqua Land Exchange Project (ULEP)
• All-H Analyzer (AHA)
• Chinook Salmon Life Cycle Model
• Salmon Lifecycle Analysis Modules (SLAM)
• Salmon Population AnalyZer (SPAZ)

Detailed descriptions of these and other population models will be in the forthcoming book:

"Pacific salmon environment and life history models: advancing science for sustainable salmon in the future" (anticipated publication date 2007, American Fisheries Society, information available online.)

4.6.1.1 Selected references

General references that provide additional information on fish population dynamics models can be accessed online >>

ISAB (Independent Scientific Advisory Board). 2001. Model Synthesis Report: An analysis of decision support tools used in Columbia River Basin salmon management. Report ISAB 2001-1. Prepared for the Northwest Power Planning Council and the National Marine Fisheries Service. Portland, Oregon.

Nielsen, L. A., and D. L. Johnson. 1983. Fisheries techniques. American Fisheries Society, Bethesda, Maryland.

Quinn, T. J., II, and R. B. Deriso. 1999. Quantitative fish dynamics. Oxford University Press, Inc., New York, New York.

4.6.2 RIPPLE Population Module

The RIPPLE Population Module follows the multi-stage stock-production approach to population modeling. In this approach, a carrying capacity and density-independent mortality for each life stage, estimated from field data or literature, are used to develop life-stage-specific stock-production relationships. The model identifies critical life-stages, and compares relative changes in population size between alternative management scenarios (e.g., various instream flows, fish passage, hatchery management, potential enhancements). The model also serves as a framework for integrating available data and can either be used predicatively or as a means of identifying critical data gaps.

The following reference is recommended for additional information on the RIPPLE Population Module:

Stillwater Sciences. 2006. Population dynamics of bull trout and spring Chinook salmon at the Carmen-Smith Hydroelectric Project, Upper McKenzie River Basin, Oregon. Final report. Prepared by Stillwater Sciences, Arcata, California for Eugene Water & Electric Board, Eugene, Oregon.

4.6.3 SHIRAZ

The SHIRAZ model allows the user to track fish populations through their life stages and habitats, and then back to the spawning grounds. A transformation function allows hatchery spawners in the river to produce natural fish (based on the input of stray rates). Stochastic variability and uncertainty in functional relationships can be introduced into the model, and then multiple simulations can be used to develop a distribution of outcomes or quasi-confidence intervals based on model assumptions. This approach can also be used to estimate species extinction risk or predict population trends over time following initiation of a habitat action. SHIRAZ runs on a Microsoft Excel platform. Currently the Muckleshoot Indian Tribe is using SHIRAZ in the Green/Duwamish Rivers and NOAA Fisheries is applying SHIRAZ to the Snohomish River.

The following references are recommended for additional information on the SHIRAZ model:

Bartz, K. K., K. M. Lagueux, M. D. Scheuerell, T. Beechie, A. D. Hass, and M. H. Ruckelshaus. Translating restoration scenarios into habitat conditions: an initial step in evaluating recovery strategies for Chinook salmon (Oncorhynchus tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences 63: 1578-1595. doi:10.1139/F06-055.

Scheuerell, M. D., R. Hilborn, M. H. Ruckelshaus, K. K. Bartz, K. M. Lagueux, A. D. Haas, and K. Rawson. 2006. The Shiraz model: a tool for incorporating fish-habitat relationships in conservation planning. Canadian Journal of Fisheries and Aquatic Sciences 63: 1596-1607. doi:10.1139/F06-056.

4.6.4 EDT

The Ecosystem Diagnosis and Treatment (EDT) approach and concept involves analysis of a patient (fish) and template (habitats). It is largely based on numeric ratings of key habitat and productivity attributes, as determined by a select group of experts familiar with the circumstances within a given basin. The six basic steps of EDT are:

1. Identify objectives
2. Perform analysis and diagnosis
3. Formulate treatments
4. Describe benefits and risks (trade-off analysis)
5. Refine project objectives
6. Apply treatments, monitor, and evaluate.

EDT and EDTlight are proprietary models developed by Mobrand Biometrics, Inc. (now MOBRAND-Jones & Stokes) to describe the relationship between quantity and quality of habitat and fish performance. This is accomplished using a detailed set of functional relationships or “rules” to generate model outputs in the form of relative abundance (capacity), productivity, and life history diversity of a focal species.

The following reference and website are recommended for additional information on EDT and EDTlight models:

Mobrand Biometrics, Inc. 1999. The EDT Method. Mobrand Biometrics, Inc., Vashon, Washington.

The Mobrand library >>

4.6.5 SALMOD

The Salmonid Population Model (SALMOD) was developed by the USGS in Fort Collins and is a computer model that simulates the dynamics of freshwater salmonids populations. As stated in the USGS software documentation (available on the link provided below), “The model's premise is that egg and fish mortality are directly related to spatially and temporally variable micro- and macrohabitat limitations, which themselves are related to the timing and amount of streamflow and other meteorological variables. Habitat quality and capacity are characterized by the hydraulic and thermal properties of individual mesohabitats, which we use as spatial "computation units" in the model. The model tracks a population of spatially distinct cohorts that originate as eggs and grow from one life stage to another as a function of local water temperature. Individual cohorts either remain in the computational unit in which they emerged or move, in whole or in part, to nearby units (see McCormick et al. 1998). Model processes include spawning (with redd superimposition and incubation losses), growth (including egg maturation), mortality, and movement (freshet-induced, habitat-induced, and seasonal).”

A user’s manual and free software download are available online >>

Bartholow, J., J. Heasley, j. Laake, J. Sandelin, B. A. K. Coughlan, and A. Moos. 2002. SALMOD. A population model for salmonids: user's manual. Version W3. U. S. Geological Survey, Fort Collins, Colorado.

4.6.6 Advantages and disadvantages of population modeling

Many population models have been developed, for a variety of fish species and locations. While each of these has different advantages and disadvantages, which are not discussed in detail here, a general list of the advantages and disadvantages of the modeling approach is provided below.

Advantages

• Level of modeling effort can be adjusted based on the amount of data available.
• Can be used as a predictive tool to evaluate project effects operating on varying temporal and spatial scales.
• Can integrate results of various studies, allowing evaluation of the relative importance of various types of project effects, and supporting management decisions that invest limited resources in correcting project impacts that substantially influence fish populations.

Disadvantages

• A large amount of data is required to run a complete model for accurate results.
• Local information may not be available; may need to make assumptions.
• Despite extensive data collection and literature review, when gathering biological input values there is always a degree of uncertainty, and a potential for error.
• Modeling results may over-simplify complicated interactions.

5.3.1 Field-based assessment of potential effects

In a field-based assessment of potential effects of the project, the wetlands in the study area are first characterized as described above, in order to gain basic information on:

• species composition,
• species assemblages or ecological zones,
• hydrological conditions, and
• soil conditions.

The assessment starts with the identification of wetlands likely to be hydrologically connected to the reservoir. This is done via remote sensing or a pedestrian and/or boat survey of the reservoir perimeter. Field indicators of hydrology and wetland conditions (e.g., surface water levels, soil saturation, natural surface flow paths and topographic relief, high water lines, debris lines, presence of wetland indicator plant species, hydric soils, and proximity to the reservoir itself) are then used to refine the assessment of hydrologic connectivity and to look for potential project effects.

The review of field-based indicators includes an assessment of whether hydrological conditions have been altered. It can be difficult to distinguish normal seasonal and annual variability in water levels and soil moisture from longer-term hydrologic alterations associated with project operations. Data on reservoir stage change is often available from the Licensee. These data can be used in conjunction with field indicators to assess whether the project has altered hydrologic conditions in a manner that is affecting wetlands. Reservoir effects will differ depending on operations. Reservoirs experiencing rapid drawdowns or widely fluctuating water levels have different effects on associated wetlands than those that maintain an artificially stable water level. Evidence of longer-term changes in vegetation are one indicator of potential project effects. Types of evidence observed in the field might include dead trees or shrubs within a reservoir fluctuation zone, or conifers encroaching into former wet meadow habitats. In addition, soils can serve as an integrator of environmental conditions over longer periods. For example, hydric soils would be predicted to be found in an area that is inundated for at least part of the year. If hydric soils are found in an area that appears to be dry throughout the year, then hydrologic conditions might have changed in the recent past. Further investigation would be required to assess whether this recent drying trend was likely caused by the project or by other factors, including natural climatic variability.

5.3.1.1 Advantages and disadvantages of approach

The field-based assessment of the effects of water impoundment effects has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• Species assemblages and species-specific information can be assessed.
• Hydrological and soil conditions can be assessed.

Disadvantages

• The effort is time-intensive; the practicality of this approach depends on the size of the assessment area.
• There are often accessibility issues.
• Multiple visits to the site may be needed in order to fully understand and assess potential effects.
• In the end, the assessment comes down to professional judgment; the evaluation is qualitative.
• There needs to be some means of defining reference conditions.

5.3.1.2 Selected references

Brinson, M. M. 1993. A hydrogeomorphic classification for wetlands. Final report. Wetlands Research Program Technical Report WRP-DE-4. Prepared for US Army Corps of Engineers, Waterways Experiment Station, Washington, D. C.

Cowardin, L. M., V. Carter, F. C. Golet, and E. T. LaRoe. 1979. Classification of wetlands and deepwater habitats of the United States. Biological Services Program Report FWS/OBS-79/31. Prepared for U. S. Fish and Wildlife Service, Office of Biological Services, Washington, D.C.

Middleton, B. 1999. Wetland restoration, flood pulsing, and disturbance dynamics. John Wiley & Sons, Inc., New York, New York.

NRC (National Research Council). 1995. Wetlands: characteristics and boundaries. Committee on Characterization of Wetlands, Water Science and Technology Board, Board on Environmental Studies, and Toxicology, Commission on Geosciences, Environment, and Resources, and National Research Council. National Academy Press, Washington, D. C.

Tallent-Halsell, N. G., and L. R. Walker. 2002. Responses of Salix gooddingii and Tamarix ramosissima to flooding. Wetlands 22: 776-785.

USACE (Army Corps of Engineers). 1987. Corps of Engineers wetlands delineation manual. Technical Report Y-87-1. USACE, Environmental Laboratory, Waterways Experiment Station, Vicksburg, Mississippi.

5.3.2 Remote sensing to assess potential effects

Another method of assessing effects of the project is to use remote-sensing, in which a time series of aerial photographs is used to evaluate changes in the wetlands through time. Aerial photographs of the site need to be available, ideally for multiple years, both pre- and post- project implementation. Furthermore, it is often useful to have aerial photography not only for the study area in question but the surrounding watershed to improve understanding of the ecological roles and significance or uniqueness of any wetlands or other sensitive habitats that might be affected by the project. Ground-truthing of images is imperative to obtain accurate assessments.

5.3.2.1 Advantages and disadvantages of approach

Remote sensing to assess the effects of water impoundment effects has advantages and disadvantages relative to the other approaches evaluated, as discussed below:

Advantages

• A large spatial area can be assessed.
• Coarse-scale changes are apparent (e.g., where a wetland changes drastically in size, or woody vegetation encroaches into an herbaceous emergent wetland).

Disadvantages

• The approach is not species-specific; in most cases changes in species composition cannot be discerned (although in some cases it is possible to detect changes in overstory species).
• The approach is dependent on the quality and resolution of the photographs; poor quality can hinder any sort of assessment of changes through time. In general, imagery (aerial photography or satellite imagery) for recent years will be much more available and of higher quality and resolution than that covering previous periods.
• Beyond gross-level changes, the approach relies on the ability to differentiate “signatures” of various wetland habitat types and to separate wetlands from upland areas. Signatures can also be used to distinguish dominant overstory species. If distinctive signatures cannot be obtained, effects are difficult to interpret.

5.3.2.2 Selected references

NRC (National Research Council). 1995. Wetlands: characteristics and boundaries. Committee on Characterization of Wetlands, Water Science and Technology Board, Board on Environmental Studies, and Toxicology, Commission on Geosciences, Environment, and Resources, and National Research Council. National Academy Press, Washington, D. C.

Wilen, B. O., V. Carter, and J. R. Jones. 2002. Wetland management and research: wetland mapping and inventory. http://water.usgs.gov/nwsum/WSP2425/mapping.html. United States Geological Survey Water Supply Paper 2425. USGS, National Water Summary on Wetland Resources.

Wilkie, D. S., and J. T. Finn. 1996. Remote sensing imagery for natural resources monitoring: a guide for first-time users. Columbia University Press, New York, New York.

6.1.1 Inventory of facilities and assessment based on professional judgment

Because of the difficulty in assessing the effects of the hydroelectric project on the populations and metapopulation dynamics of a variety of wildlife species, professional judgment can be used to assess whether project facilities are likely to interfere with movements or result in injury or mortality of animals. This approach is best suited for projects at which crossing opportunities (e.g., bridges, underpasses) do not currently occur or are limited. This type of approach involves the following steps:

• Review the scientific literature and consult with species experts to gather information on the habitat associations and movement patterns of species of interest.

• Map general terrestrial habitat and potential barriers to wildlife movement, ideally in a GIS database.

• Perform a field survey using the map from the preceding task to evaluate the site-specific level of habitat fragmentation, assess the risk of entrapment in diversion canals, and identify potential sites for installing wildlife crossing structures.

• In some cases, develop a program for testing or monitoring the effectiveness of crossing structures.

• Use professional judgment to analyze the likely effects of Project features on wildlife movements and the potential benefits of installing wildlife crossings.

This method has been applied at the North Umpqua Hydroelectric Project (FERC Project No. 1927), on the Umpqua River, Oregon.

6.1.2 Field study of wildlife movement

At projects where crossing opportunities (e.g., bridges over diversion canals, culverts, or under project roads) already occur, the use and effectiveness of wildlife crossings can be analyzed by field studies that document wildlife movement. Sites should be selected based on levels of wildlife activity evident at the entrances and exits of crossings or on the crossing themselves (e.g., tracks, scats, worn trails), likelihood of use based on crossing placement and characteristics (e.g., condition of vegetation and cover at entrance and exit, quality of surrounding habitat, topography, crossing design), and feasibility of monitoring (e.g., adequate camera placement, suitability for tracking surface installation). Initial steps in this type of study involve basic habitat and facility mapping and a field inventory of project features described above. Next, sites are selected for field monitoring.

Field sampling conducted over a period of time can capture seasonal variations in wildlife use of crossing structures. Passive sampling can be conducted using methods such as motion/heat sensing cameras that are triggered as an animal passes by, and sand pits or soot plates to record wildlife tracks (Figure 17).

Analysis of the data can provide information on:

• the species or general taxa (and when possible, the gender, age class, and condition of individuals) that may be affected by project-created barriers;
• the frequency and temporal pattern of crossing events; and
• whether use differed among crossing types locations, or other variables.

Also, animal use of potential crossings at hydroelectric projects could be studied by marking or tracking individual animals (e.g., with PIT tags or other markers, or using radio telemetry) to document their movement patterns. This approach would be more intensive and expansive than the passive use of cameras or track plates described above.

Radio tracking of fishers has been applied by the Forest Service, Rogue River, Oregon (Aubry et al. 1997) and cameras have been used to document martens at the Skagit River Hydroelectric Project (FERC Project No. 553), Skagit River, Washington.

6.2.1 Professional judgment assessment

A professional judgment assessment can be developed to determine if project features are creating obstacles and barriers which prevent the movement of wildlife species through aquatic and riparian habitats. This process is based on findings from literature reviews and field surveys of project features. In addition, coordination with wildlife species experts can provide valuable information about distribution, habitat requirements, and potential effects of management activities on wildlife species. Typical hydroelectric facilities that can be evaluated include the following: dams, reservoirs, flows in bypass reaches and full-flow reaches, diverted and intercepted tributaries, culverts and road or waterway/stream crossings, disturbances to riparian vegetation, roads and waterways in riparian areas, changes to water quality, and modifications of natural obstacles.

6.2.2 Field study of amphibian movement

A mark-recapture study can be conducted above and below potential barriers (i.e., dams, culverts, roads, regulated reaches) to provide information as to whether the barrier prevents amphibian movement. Individual juvenile and adult amphibians can be identified, or “marked” by either photographing chin patterns or inserting passive integrated transponder tags under an individual’s skin. Chin patterns of foothill yellow-legged frogs, for example, are unique to each frog, as fingerprints are to humans, and once developed are maintained throughout the life of the frog, although they can be more or less distinct under various conditions. Photographs can be used for comparison with future amphibian captures, thereby documenting the movement of individual frogs. PIT tags can also be used to mark and monitor the movements of individuals. Surveys should be preformed during the season that the amphibians would be expected to move (e.g., just prior to egg-laying period, at the end of the breeding season when they are preparing for hibernation or dormancy). Initial surveys should be conducted for several consecutive days with the intent of marking as many frogs as possible. Recurring surveys above and below the barrier should take place periodically, and should consider the efforts of weather on the timing of movement patterns. Results of this study can determine if the barrier being studied is preventing amphibian movement on a daily or seasonal basis.

This method has been proposed but not yet implemented for Pacific Gas and Electric DeSabla–Centerville Project (FERC Project No. 803), West Branch Feather River and Butte Creek, California. Monitoring amphibians and reptiles with PIT tags has occurred all over the world, including New Zealand.

Beausoleil, N. J., D. J. Mellor, and K. J. Stafford. 2004. Methods for marking New Zealand wildlife: amphibians, reptiles, and marine mammals. Department of Conservation, Wellington, New Zealand.

6.4.1 Comparison of regulated and unimpaired flow and temperature patterns

The main objectives of the office-based analysis is to compare data collected during amphibian surveys (i.e., water depths, flows, velocities, and temperatures) to breeding activities and amphibian habitat microhabitat conditions under unimpaired and regulated flow scenarios. Differences in hydrograph between synthesized unimpaired and regulated flow can be analyzed for daily average flows for the entire water year, and also for the time periods that represent amphibian life stages (i.e., breeding, tadpole development). As a result, temperature and flow data can be plotted to correspond to amphibian life stages. By plotting mean daily water temperature and flow over time, it is possible to superimpose amphibian breeding timing and determine mean daily water temperatures and flow conditions. Relative abundance data, as a measured value of number of individuals over time and area surveyed, will be calculated for each life stage (number of larvae will be estimated). Species-specific analysis of potential limiting factors will be performed, including evaluation of the amount of algae and diatoms present for tadpole forage, the amount of cover or shading provided by margin and riparian vegetation, and the type of potential predators present. An analysis of average daily flow and temperature fluctuations under synthesized unimpaired and regulated hydrology can be used to indicate higher and lower potential for stranding and desiccation during breeding and tadpole rearing periods, potential for scour of eggs, and determining above or below threshold temperatures for breeding or rearing.

This method has been applied at the South Feather Power Project (FERC Project No. 2088), South Feather River, California.

6.4.2 Amphibian habitat mapping under test flows

The approach to the amphibian habitat mapping under test flows is similar to habitat mapping described for fish species in Section 4.1.4. The test flow study can be conducted at sites where amphibians (eggs or tadpoles) are observed during surveys and where flow can be controlled by the Project. Monitoring amphibian habitat during a variety of flow releases (e.g., 20 cfs, 50 cfs, and 100 cfs) can determine the following:

• effects of flows on breeding habitat (egg-laying and tadpole-rearing),
• where and how much suitable habitat occurs at the lowest test flow release, how the characteristics of that habitat change at each subsequent (increased) flow release,
• and where and how much suitable habitat occurs at each of the test flows under consideration.

Habitat polygons are identified based on field observations of egg deposition and tadpole rearing, literature review, expert opinion, and professional judgment. Characterization and quantitative analysis of physical habitat (i.e., depth, velocity, substrates and vegetation cover) is determined to be suitable or unsuitable for each life stage under each flow (i.e., Seltenrich and Pool 2001, Kupferberg 1996a). A qualitative assessment of each polygon is evaluated based on the professional judgment to define the polygon as high, medium, or low quality, or unsuitable. Flow releases should be conducted after special-status amphibian breeding is completed, to limit any potential impacts on amphibian populations.

This method has been applied at many locations throughout the world, such as Sacramento Municipal Utility District, Upper American River Project (FERC Project No. 2101), American River, California.

6.4.3 Two-dimensional hydraulic modeling of amphibian habitat

Conducting a 2D hydraulic model can evaluate Project flow related effects on amphibians, similar to the approach used to evaluate habitat for fish species described in Section 4.1.3. The results of the model can be used for the hydraulic simulation and habitat modeling. The output from this model provides site-specific WUA in ft2 for each amphibian life-stage analyzed. The following steps describe the process of creating a 2D hydraulic model:

1. Compile and review existing information.
2. Identify potential habitat and select survey sites by using aerial photographs, low-level video photography, USGS 7.5 minute topographic maps, or habitat mapping from instream flow studies.
3. Compare to available information on species-specific habitat criteria and documented habitat characteristics (e.g., Jennings and Hayes 1994, Stebbins 2003).
4. Conduct surveys following the methods of current species-specific protocols.
5. Evaluate effects and 2D hydraulic modeling at each lifestage (eggs, tadpoles, juveniles, and adults) using data and/or results from following studies:

• Results from the Hydrology Study and Project Operation Model development which will provide information on unimpaired and regulated stream flow, ramping rates, reservoir operating levels, and reservoir and diversion dam spill frequency, timing, and duration
• Results from the Water Temperature Study to evaluate how hydroelectric project facilities and operations affect temperatures in project-affected reaches
• Data from the Fish Population Study to evaluate the presence, distribution, and abundance of potential predators on amphibians
• Data from the Benthic Macroinvertebrate Study to evaluate the distribution and abundance of suitable prey taxa
• Data collected on algae and diatoms, riparian vegetation, and predator assemblage will be utilized for a limiting factor analysis

Licensee can conduct 2D hydraulic modeling, ideally one representative site, that all four lifestages have been observed to occupy. Development of a Habitat Suitability Criteria for all amphibian lifestages is necessary for the implementation and success of 2D modeling. Weighted Usable Area curves are proposed as the final product of analysis in the 2D model.

This method has been proposed but not yet implemented for Pacific Gas and Electric DeSabla–Centerville Project (FERC Project No. 803), West Branch Feather River and Butte Creek, California.

7.1.1.1 Recreation facility inventories

Facility inventories involve organizing information about the number, size, condition, and characteristics of recreation facilities such as campgrounds, boat launches, day use areas, restrooms, interpretive kiosks, and so on. Study reports typically include summaries and associated databases linked to GIS maps; they may also include information about

1. seasonal availability to the public,
2. American Disabilities Act (ADA) accessibility,
3. current biophysical conditions (if relevant), and
4. current level of maintenance and management.

In general, however, these studies produce basic catalogs of facilities that exist rather than evaluations of their adequacy (ADA compliance is the obvious exception).

Many agencies have developed facility inventory protocols (e.g., types of campgrounds, toilets) and standards for assessing “condition classes” of dispersed recreation sites or other facilities. There is also a substantial literature on how to inventory and assess effects at dispersed areas (Cole 1987, Marion 1995). In general, these studies are executed by recreation staff in the field, and do not involve surveys of users about perceived conditions. They are often conducted at a relatively basic “rapid assessment” level, but sometimes more detailed and precise information about sites or facilities are judged necessary and require greater effort.

7.1.1.2 Access inventories

In contrast to facility inventories that focus on specific sites and development, access inventories summarize linear recreation developments such as roads and trails. Reports provide summaries and databases with specific descriptive information, typically with links to GIS-based maps. As with facilities, many agencies have specific protocols for classifying types and conditions (including ADA accessibility classification). Similarly, these inventories are typically conducted by recreation staff in the field without input from users; they are not intended to assess the adequacy of conditions for certain types of opportunities (see below).

7.1.1.3 Existing use inventories

Recreation use information provides a starting point for examining visitor impact and conflict issues. The recreation capacity concept suggests that impacts may be related to use, and standards that define unacceptable impact levels can help define how much use is too much. Thirty years of capacity research has shown that other factors affect impacts (giving rise to limits of acceptable change [LAC] and similar frameworks), but use information remains an important variable.

Most recreation use information is collected for large areas (e.g., at the forest level) or for long periods of time (e.g., for the entire year), giving little insight into impacts during specific times or at specific locations. For most relicensing efforts, it is important to focus on more specific use measures, each of which must specify timing (e.g., at one time, per day, per week, per month, per season), location (e.g., at a launch area, in the entire segment, at specific attraction sites), and units (e.g., user days, people, or trips). Options for collecting existing use information at different levels of precision include

1. mandatory registration systems (i.e., permits) and developed site use from fee receipts;
2. “full” use monitoring programs where systematic on-site observation efforts and mechanical (trail and vehicle) counters are integrated; or
3. a more “limited” use monitoring program that focuses on voluntary registrations, some spot monitoring to validate assumptions, and “opportunistic” or “indirect” observations of indicator variables (e.g., parking lot vehicle counts) requiring less time and expense, but which would help improve estimates.

There are substantial trade-offs among these options in terms of precision vs. cost, and appropriate choices depend upon the nature of the management issues and characteristics of use and the area. Starting points for literature on use monitoring includes Shelby and Heberlein (1986) and Watson et al. (2000).

7.1.1.4 Use trends and future demands

Information about potential future recreation use (e.g., demand) is also relevant in relicensing. Future use is sometimes estimated by summarizing current use and applying national or regional recreation trend information (e.g., the National Survey on Recreation and the Environment; the Outdoor Industry Association survey on human-powered outdoor activities, state-by-state trend information usually developed in mandated Statewide Comprehensive Outdoor Recreation Plans or SCORPs).

However, this method may not be viable for river reaches that do not have current use (due to a lack of flows or access), or for predicting use of reaches or reservoirs whose characteristics will be modified by new hydropower development or operations. Efforts to estimate this demand generally require professional judgment and/or demand “experiments,” in addition to a review of trend information, but may also include analysis of survey responses to questions about future use (recognizing that intentions are not always good predictors of behavior). A starting point for literature on recreation use trends includes Cordell et al. (2000).

7.1.1.5 Trip and user characteristics

Studies that characterize existing users and the kinds of trips they take are often as important as use information. These studies typically involve survey-based methods (including focus groups, structured interviews, or user surveys), and are most effective when organized by types of opportunities. Reports summarize variables such as group size, trip length, group composition, numbers of vehicles, numbers and types of boats or other equipment, activity participation, and socio-demographics (age, gender, education, etc.).

A common shortcoming in recreation survey reports is that user and trip characteristics may be organized around broad activity types rather than more specific opportunities. For example, one can’t really manage effectively for “fishing” without further specifying the species (e.g., trout), technique (e.g., wading-based fly angling), and perhaps other important attributes (e.g., in a low density, primitive setting), so it often makes sense to disaggregate survey respondents by more specific groups, particularly as this information is used to compare evaluation variables (see below).

There is a substantial literature on survey research (e.g., Fowler 1993, Nunnally and Bernstein 1994, Dillman 2000) with less work specifically focused on recreation survey methods (Whittaker et al. 1998). Many “standard” use and trip characteristic questions are in common circulation, and it pays to use tested items when those are available (particularly as they can facilitate comparisons across studies). Decisions about survey sampling (e.g., systematic on-site sampling vs. time-based cluster sampling) and survey mode (e.g., mail vs. on-site vs. telephone), among other survey methods issues, need to be considered on a case-by-case basis depending upon the characteristics of use and the area. As survey method issues become more complex and the level of resolution needs to be more precise, it is more important to involve experienced or trained survey researchers.

7.1.1.6 Regional recreation inventories and context

Sometimes it is useful to understand regional recreation opportunities to provide context for those being considered in the project area. For instance, are the opportunities in question relatively rare and in high demand, or are they more ubiquitous and only moderately popular? These types of studies are generally conducted at a “rapid assessment” level through reviews of secondary sources such as guidebooks and large-scale resource management documents (e.g., a forest plan). Reports typically provide database summaries and links to regional maps.

7.2.1 Flows and recreation

>> See the 2005 "Flows and recreation" guide, a full publication on this issue.

Instream flow—the amount of water in a river or stream—has a profound influence on the type and quality of river recreation opportunities. A substantial literature addresses the short and long-term flow requirements for fisheries, aquatic habitat, riparian communities, geomorphic features, or other biophysical attributes (Hill et al. 1991, Richter et al. 1997, Tharme 2002), all of which can affect recreation (Whittaker et al. 1993). A smaller but developing literature on flows for recreation more commonly focuses on “immediate” rather than long-term effects (Brown et al. 1991, Whittaker et al. 1993, Whittaker and Shelby 2002, Whittaker et al. 2006). Most of this work addresses whitewater boating, although some studies have examined flow effects on general recreation (Narayanan 1986, Duffield et al. 1994), swimming (Whittaker and Shelby 2001), availability of beaches (Shelby et al. 1992), in-channel “slot canyon” hiking (Shelby et al. 1997), or general river aesthetics (Whittaker and Shelby 2002).

Most flow-recreation studies in relicensing settings use on-site assessments by panels of experienced users (e.g. boaters or anglers), particularly when flows can be experimentally controlled. However, there are many other ways to examine these issues depending upon the river’s characteristics.
The following report provides a complete evaluation of the scientific approaches to evaluate the effect of hydroelectric dams on recreation opportunities.

Whittaker, D., B. Shelby, and J. Gangemi. 2005. Flows and recreation: a guide to studies for river professionals. Whittaker, Shelby, & Gangemi, and the Hydropower Reform Coalition, Washington, D. C.

7.2.2 Reservoir levels and recreation

There has been less work on the effects of reservoir levels than flows, but this topic may also be important in some relicensings. Reservoir levels can affect boatability, access to fishing or other sites, boat stranding, facility use (boat ramps), and aesthetics (“bath tub ring”).

Methodological options and considerations are similar to those for flow-recreation studies, and might typically involve user surveys or interviews, although reservoir users in general appear to be less sensitive to fluctuation changes than many river users. If the reservoirs don’t fluctuate much (but you still want to know how changes would affect recreation), you may have to employ other techniques (e.g., having users rate computer-simulated views or descriptions of how features would change), or resort to professional judgments based on previous studies and information on how the reservoirs are used.

7.2.3 Facility need assessments

This is the evaluative side of the equation regarding facilities; it complements inventory information. In these studies, professional judgment or user surveys are typically employed to evaluate the type, amount, and condition of existing facilities for condition and amount. This involves a standard assessment of facility adequacy, usually with a focus on type and amount, maintenance level, safety/liability, ADA compliance, etc. Some are assessed by professional judgment or state of the art (safety, ADA). Others may involve assessments from current users—usually using survey techniques that follow normative theory, with analysis links to types of opportunities. More sophisticated analyses identify how different groups revaluate facility needs by their type of opportunity.

7.2.4 Use conflicts

User conflicts at recreation settings occur when one group is sensitive to particular impacts from another group. Conflicts typically occur between groups involved in separate activities in the same area, but may refer to sub-groups doing the same activity in some different way. In many cases, conflicts are asymmetric (one group has antipathy toward another, but not the reverse).

There is well developed literature that discusses conflicts in terms of goal interference, norm theory, and larger cognitive hierarchy theory, and some conflicts appear to be more value-based than others. Appropriate studies try to identify sensitive and offending groups and may explore underlying reasons for the antipathy, usually through such means as focus groups and user surveys.

7.2.5 Recreation capacity assessments

Addressing the tension between use and protection continues to be a management and research challenge. How much is too much is a recurring theme in recreation management. There is a considerable literature on capacities and visitor impacts.

In general, however, these issues are addressed through focus groups and user surveys to prioritize indicators, set standards, and review acceptability of management actions. Social impact information is usually collected via surveys that ask users to report the impact levels they experienced and the levels they will tolerate. Surveys also can provide information about which impacts are most important (helping winnow the number of indicators), and show relationships between use and impacts (when coupled with a use monitoring program).

It is possible to develop some kinds of social impact information without conducting a full user survey, particularly if the goal is only to prioritize indicators or develop standards. For example, expert judgments based on a literature review of priorities and standards from other rivers (potentially during an intensive “indicators and standards” workshop with stakeholders) may be sufficient in situations where controversy levels are low. A few capacity issues in relicensing settings may well fit this description, but the contentiousness of others may require more rigorous data collection and analysis.

Analysis needs to occur for disaggregated user groups (e.g., boaters, backcountry anglers, hikers) to allow comparisons that can help “triangulate” results or accurately characterize group differences. When different groups show diverse results, studies should be careful not combine them to represent “all users.” This is the common strategy for informing decision-makers when there is diversity in a user population; results are used to describe how various decisions would affect different groups, not tally “votes” for any particular action. As discussed throughout this section, organizing information by opportunity is usually critical in these efforts.

7.2.6 Recreation economic studies

Economists study the costs and benefits of individual, collective, and institutional decisions, and examine how those decisions affect the well-being of individuals or society. In general, economists define “benefit” as “anything contributing to an improvement in condition” while “cost” is a “loss, sacrifice, or detriment.” Because the range of benefits and costs can be enormous, much of the work in economics focuses on assessing that range using a single metric (dollars).

In recreation management contexts, recurring economic issues focus on

1. the cost to build and maintain recreation facilities,
2. the estimation of recreation demand,
3. the economic effect of recreationists’ expenditures on local and regional economies,
4. the willingness of recreation users to pay fees for use of facilities or access to recreation areas, and
5. the value of recreation opportunities in a broader welfare economics model (Loomis and Walsh 1997).

It is important to recognize that use value is not the only economic issue involved in assessing the value of whitewater boating. Other types of economic value information that may also apply include:

• Local economic effects. These effects are associated with expenditures of boaters while participating in an activity (e.g., food, lodging, gas, equipment, shuttles, etc.). The effects of increased boating in a small region or local area can be significant if use levels are high and alternative recreation opportunities in the area are few (Loomis and Walsh 1997). From a national or large regional perspective, however, boater expenditures associated with a single river are essentially negligible because boaters would spend similar amounts of money running another river or doing another activity in the same large region even if the study river was unavailable (Loomis and Walsh 1997).

• Option, bequest, and existence value. These focus on the value of river opportunities for people who are not currently using the resource, but who might (1) want to use it in the future (option value), (2) want future generations to be able to use it in the future (bequest value), or (3) appreciate the existence of those opportunities even if they will never use them (existence value).

9.1.1 Review of existing data

Existing information on cultural resources may be available from a variety of sources. The SHPO for the state containing the project typically maintains databases of recorded archaeological sites, historic structures surveys, and traditional cultural properties in the state, as well as cultural resources projects that have been conducted in the state. Other sources of existing information may include the records of federal agencies that have land in the project APE, records of the hydroelectric project operator, Tribal cultural resources programs and other Tribal entities, local and regional historical societies, and regional universities.

9.1.2 Pedestrian surface surveys

Pedestrian surveys can be used to locate any surface-visible evidence of cultural resources in the project area. A surface survey is normally required unless the area has been previously examined using techniques that meet current professional standards established by the SHPO. These standards may vary from state to state, and may be augmented to include requirements of federal agencies that administer lands in the project APE. This technique involves the systematic inspection of the entire project APE (with the exception of impassable and hazardous areas) by establishing and walking transects at specified intervals. Survey strategies may also be designed around established site predictive models, which may focus on examining environmental settings known to have a high potential for cultural materials.

Survey crews can establish transects, but may also pursue opportunistic routes to maximize observation of mineral ground exposures. Surveyors may also scrape organic duff aside on the ground to provide additional exposure of mineral soil to increase the potential for detections. All surface-evident archaeological sites, features, and artifacts, as well as historic built resources and potential traditional cultural property locations, are recorded and mapped, along with other pertinent observations. Previously recorded archaeological sites and isolated finds should be relocated and visited during this inventory survey.

9.1.3 Subsurface archaeological site discovery probe investigations

Surface surveys will fail to detect artifacts on ground surfaces obscured by vegetation and organic duff. In addition, the deposition of organic materials contributes to soil development, which can bury cultural materials, leaving few artifacts on the current ground surface. In these situations, subsurface site discovery tests can provide a small sample of buried soil, and can augment surface inventory efforts. Site discovery shovel probes are best used to examine landforms likely to contain archaeological sites and areas that are likely to be affected by project-associated activities. Subsurface site discovery investigations may also focus on examining areas identified as isolated finds during surface surveys, to determine whether the find was part of a larger obscured archaeological site.

9.1.4 Evaluation of archaeological resources

Identified archaeological resources should be evaluated for eligibility to the NRHP. Sites that are determined to be not eligible to the NRHP are not considered in the Section 106 process, but sites that have not been evaluated must be considered eligible for the NRHP and protected under Section 106 until the site is evaluated.

Criterion ‘d’ of the NRHP criteria of evaluation (36 CFR Part 60.4) is most commonly used for evaluating the significance of archaeological sites, deeming as significant those properties with sufficient integrity “that have yielded, or may be likely to yield, information important in prehistory or history.” A site’s significance, therefore, lies in its proven or potential ability to make important contributions to the “theoretical and substantive knowledge of the discipline” (Butler 1987), either to regional culture history or to broader questions of human behavior. Site size, artifact numbers and densities, artifact diversity, and the presence/absence of cultural features, contribute to the ability of a site to yield important information, but NRHP significance is not limited by these quantitative measures.

The SHPO may have established guidelines or standards for assessing NRHP significance and these should be followed if available, since the SHPO must concur with eligibility determinations. In many states, subsurface test excavations are required at archaeological sites to fully assess the structure and information potential of the site. In general, archaeological investigations should be sufficient to establish site size (surface and subsurface), structure, content, integrity, and quality/condition of site data.

9.2.1 Inventory methods

A primary source of information on built resources will likely be the records and archives of the hydroelectric project operator. These data should provide information on when the various project buildings and structures (e.g., dams, canals, flumes, etc.) were constructed and may include architectural drawings and/or photographs documenting the original appearance of the resources. Information on other built resources in the APE may be available in these records as well, or may be found in SHPO files or local and regional historical societies.

The historic preservation specialist then conducts a field inspection to document the current condition of all known built resources. Unrecorded built resources may also be encountered and documented during this inspection or may have been observed during the archaeological pedestrian survey.

9.2.2 Evaluation methods

All historic built resources that are at least 50 years old should be evaluated for NRHP significance and eligibility. Again, under Section 106, unevaluated resources must be protected as if they were NRHP-eligible. The integrity of the built resources can be assessed by comparing their current condition and setting with their documented (or inferred) original construction and appearance. Modifications and alterations should be identified and assessed as to whether they have altered the overall character of the resource.

The significance of built resources are usually evaluated under criteria ‘a,’ ‘b,’ or ‘c’ of the NRHP criteria of evaluation (36 CFR Part 60.4), so the evaluated resources may be determined significant because of (a) their association with “events that have made a significant contribution to the broad patterns of our history,” (b) their association with “the lives of persons significant in our past,” or because (c) they “embody the distinctive characteristics of a type, period, or method of construction, or that possess high artistic value.” Under criterion ‘c’ a group of resources together also may “represent a significant and distinguishable entity whose components may lack individual distinction.” Preparation of a historic context statement that places the hydroelectric project and the built resources into local and regional historical development is essential to adequately evaluate the resources under these criteria.

The SHPO often employs a standard Section 106 documentation form and/or determination of eligibility (DOE) form for built resources and these should be used. Established SHPO documentation guidelines or evaluation standards should also be followed.