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.