Appendix D. Hydraulic and Habitat Suitability Analyses Technical Memorandum

Transcription

1 Appendix D Hydraulic and Habitat Suitability Analyses Technical Memorandum

2 Draft Technical Memorandum Yankee Fork Habitat Improvement Projects: Pond Series 2 and Pond Series 3 Hydraulic and Habitat Suitability Analyses Prepared for Bureau of Reclamation December 2011 Boise, Idaho Prepared by COPYRIGHT DECEMBER 23, 2011 BY CH2M HILL, INC.

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4 Contents Section Page Hydraulic and Habitat Suitability Analyses Introduction Limitations of this Analysis Habitat Suitability Metrics Used in the Analysis Explanation of Hydraulic (Velocity and Depth) Suitability Curves Explanation of Substrate Suitability Metric Explanation of Cover Suitability Metric Combining the Four Suitability Rasters What Are the Existing Fish Habitat Conditions in Terms of Quality, Quantity, and Usage? Velocity Suitability Depth Suitability Substrate Suitability Cover Suitability Combined Suitability under Existing Conditions What Are the Quantitative Biologic Objectives of Any Proposed Actions? Analysis of Project Habitat Impacts Explanation Interpretation of Results References... 8 Exhibits 1. Concept Designs Used for Habitat Analysis (A) Pond Series 3 (B) Pond Series 2 2. Juvenile Chinook Habitat Suitability Criteria Used in this Memorandum (based on Maret, et al., 2006) 3. Exceedance Hydrograph Showing that 650 cfs Fish Flow Represents a Relatively High but Sustained Spring Flow 4. Velocity and Depth Suitability Curves from Raleigh (1986) 5. Existing Condition Velocity Suitability (A) Pond Series 3 (B) Pond Series 2 6. Existing Condition Depth Suitability (A) Pond Series 3 (B) Pond Series 2 Based on the Maret et al. (2006) Depth Suitability Curve 7. Existing Condition Depth Suitability (A) Pond Series 3 (B) Pond Series 2 Based on the Raleigh et al. (1989) Depth Suitability Curve 8. Existing Condition Substrate Suitability (A) Pond Series 3 (B) Pond Series 2 9. Existing Condition Cover Suitability (A) Pond Series 3 (B) Pond Series Existing Condition Combined Suitability (A) Pond Series 3 (B) Pond Series Pond Series 3 Velocity Habitat Suitability (A) Proposed (B) Difference 12. Pond Series 3 Depth Habitat Suitability (A) Proposed (B) Difference Based on Maret et al. (2006) 13. Pond Series 3 Depth Habitat Suitability (A) Proposed (B) Difference Based on Raleigh et al. (1989) 14. Pond Series 3 Substrate Habitat Suitability (A) Proposed (B) Difference 15. Pond Series 3 Cover Habitat Suitability (A) Proposed (B) Difference 16. Total Existing Cover Habitat and Proposed Conditions 17. Pond Series 3 Combined Suitability (A) Proposed (B) Difference COPYRIGHT DECEMBER 23, 2011 BY CH2M HILL, INC. III

5 CONTENTS, CONTINUED 18. Tabular Summary of Combined Habitat Suitability in Existing and Proposed Conditions Digital Attachments A. Mapbook for Pond Series 3 Showing Habitat Scores for the Existing Condition, Proposed Condition, and Difference B. Mapbook for Pond Series 2 Showing Habitat Scores for the Existing Condition, Proposed Condition, anddifference IV COPYRIGHT DECEMBER 23, 2011BY CH2M HILL, INC.

6 Acronyms and Abbreviations C degrees Celsius BPA Bonneville Power Administration cfs cubic feet per second fps feet per second GIS geographic information system Hg mercury ISRP Independent Scientific Review Panel mm millimeter PHABSIM Physical Habitat Simulation System Reclamation Bureau of Reclamation Se selenium Simplot Simplot Corporation Tribes Shoshone-Bannock Tribes TU Trout Unlimited COPYRIGHT DECEMBER 23, 2011 BY CH2M HILL, INC. V

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8 DRAFT TECHNICAL MEMORANDUM Hydraulic and Habitat Suitability Analyses 1. Introduction The Bureau of Reclamation (Reclamation) and Bonneville Power Administration (BPA), in conjunction with Simplot Corporation (Simplot), Trout Unlimited (TU), and the Shoshone-Bannock Tribes (Tribes), are working together to implement habitat improvement projects on the Yankee Fork, a tributary to the Salmon River in central Idaho. Two projects, Pond Series 2 and Pond Series 3, are the focus of the current efforts (Exhibit 1). The primary goal of the proposed projects is to provide high-flow refuge and year-round rearing habitat for juvenile Snake River Chinook salmon (Oncorhynchus tshawytscha). The projects are also expected to improve holding and spawning habitat for returning adult Chinook salmon, as well as habitat for Snake River steelhead (O. mykiss) and other native salmonids, including bull trout (Salvelinus confluentus). In 2008, the Independent Scientific Review Panel (ISRP) posed a series of eight questions about the potential restoration activities being considered for the Yankee Fork. The questions addressed prioritization, monitoring, permitting, contamination, and the habitat benefits of the program. The two habitat-specific questions included the following: 3. What are the existing fish habitat conditions in terms of quality, quantity, and usage? 4. What are the quantitative biologic objectives of any proposed actions? In this technical memorandum, we describe one quantitative approach that could be used to help answer these questions, and we propose some initial answers to the questions. Our approach combines quantitative habitat suitability criteria with site-specific information resulting from hydraulic, sediment, geochemical, and fisheries analyses related to the two habitat improvement projects (CH2M HILL, 2011a, b, c, d [all in progress]). The easiest way to view and understand the results and interpretations of these suitability analyses is digitally by toggling back and forth between the existing, proposed, and difference maps for each pond series using Adobe Acrobat Reader. The results are organized in this way in two digital mapbooks included as digital Attachment A (Pond Series 3) and Attachment B (Pond Series 2) to this document. In addition, selected results are included in the figure set of this report as they are referenced by the text. 1.1 Limitations of this Analysis Our approach provides a useful quantitative and spatial tool to assess the potential benefits of the two proposed projects, but there are limitations to the approach. First, the categories of habitat suitability that are quantifiable (i.e., velocity, depth, substrate, and cover) address many important habitat requirements, individually and together, but they are not comprehensive. For example, critical factors not included in the analysis include potential effects of mercury (Hg) and selenium (Se), food availability, and temperature. Also, no habitat suitability metrics are available to quantify important project benefits, including increased aeration, geomorphic complexity, and wood and cover densities. Because of this, the quantitative benefits shown by the calculations in this technical memorandum do not fully reflect the benefits of the proposed projects. Second, because this analysis characterizes habitat spatially, rather than temporally, the calculations fail to account for a primary goal of the pond series projects: improve fish access to both pond series at more flows. The results we present and discuss below show a mixed response in habitat quality resulting from introducing more flow into the two pond series. When reviewing and interpreting the results, the goal to create more access to the two pond series should be considered along with secondary benefits of improving habitat suitability within the pond series themselves (CH2M HILL, 2011e in progress). COPYRIGHT DECEMBER 23, 2011 BY CH2M HILL, INC. 1

9 HYDRAULIC AND HABITAT SUITABILITY ANALYSES DRAFT TECHNICAL MEMORANDUM 2. Habitat Suitability Metrics Used in the Analysis To quantify existing hydraulic and habitat conditions and the change that would occur with the habitat improvements projects, we selected habitat suitability metrics that could be mapped using hydraulic model results and field observations. Exhibit 2 summarizes the four suitability indices used in this analysis: velocity, depth, substrate and cover. We then converted model results into high resolution raster maps showing the spatial variability. Model results associated with a flow of 650 cubic feet per second (cfs) in the mainstem Yankee Fork were used to compute habitat suitability for existing and proposed conditions, except for the prediction of future substrate, which is based on the 2-year flow; see the Yankee Fork Habitat Improvement Projects: Pond Series 2 and Pond Series 3, Explanation of Hydraulic Modeling Draft Technical Memorandum (CH2M HILL, 2011a in progress) for more detailed explanation of hydrology. In summary, a flow of 650 cfs was selected as the fish flow for these suitability calculations because it represents a relatively high-flow value that, in a typical year, is exceeded for a sustained period of time during the spring and early summer (Exhibit 3), a time during which both pond series are designed to provide rearing habitat for juvenile Chinook salmon. 2.1 Explanation of Hydraulic (Velocity and Depth) Suitability Curves Data presented in Maret et al. (2006) were used to develop habitat suitability curves for velocity and depth, as shown in Exhibit 2. These curves were developed for a regional scale habitat suitability analysis using the Physical Habitat Simulation System (PHABSIM) model (Waddle, 2001). The source document appears to indicate that the suitability curves were chosen based on professional judgment supported by data: The fish species HSCs selected for this study were developed in the Pacific Northwest and Idaho. (Maret et al., 2006., p. 10); however, the details of the derivation of these curves are not explained. A similar, but better documented set of hydraulic suitability curves was provided by Raleigh et al. (1986), which Maret et al. (2006) cite as a primary source of their suitability curves. The curves provided by Raleigh et al. (1986) (Exhibit 4) are not the same as those used by Maret et al. (2006) (Exhibit 2). In particular, an important difference exists in the depth suitability plots: the Maret et al. (2006) implies that habitat improves with increasing depth up to 2 feet deep; at flows greater than 2 feet, habitat value remains a maximum (Exhibit 2). By contrast, the Raleigh et al. (1986) depth curve implies that habitat suitability reaches a maximum between 1 and 2 feet water depth, and habitat quality declines for deeper water (Exhibit 4). Habitat quality might be considered by some to reach a maximum at some intermediate depth (1 to 2 feet) 1, but for consistency with previous studies, we used the Maret et al. (2006) depth suitability index curve to compute the raster maps shown in this technical memorandum. In addition, an optimal depth between 1 and 2 feet does not account for another advantage of deeper water, which is a resistance to freezing deep pools. This is an additional benefit to very deep water, which is not accounted for with the Raleigh et al. (1986) suitability curve; although the Maret et al. (2006) curve does not intentionally incorporate this benefit, it does so incidentally. For comparison, we performed the depth suitability calculations using both the Raleigh et al. (1986) curve and the Maret et al. (2006) curve. For the velocity calculations, because the Maret et al. (2006) and Raleigh et al. (1986) 1 There are indirect physical and hydraulic properties (correlated to an increase in depth beyond a certain point) that might not represent the most optimal conditions for growing juvenile Chinook salmon. Increasing depths (beyond a certain point) in most cases would result in reduced velocities and decreased levels of dissolved oxygen in the water column. Other physical properties correlated to depth (e.g., temperature, photic levels, diminished scour of benthic substrate) likely contribute to the decreasing depth value beyond a certain point. In turn, the Raleigh (1986) depth suitability curves (although not used in this analysis) might more accurately depict the benefits for juvenile Chinook salmon associated with depth. 2 COPYRIGHT DECEMBER 23, 2011 BY CH2M HILL, INC.

10 HYDRAULIC AND HABITAT SUITABILITY ANALYSES DRAFT TECHNICAL MEMORANDUM curves have similar shape, with a maximum habitat value at between 1 to 2 feet per second (fps), we only made the computation using the Maret et al. (2006) curves 2.2 Explanation of Substrate Suitability Metric We considered the presence of Hg indirectly in this habitat analysis using a substrate suitability metric. Juvenile Chinook salmon tend to prefer cobble and gravel substrate during winter, but this is not a main control on habitat quality (Reclamation, 2011). In this project, however, substrate is more important because of the presence of detectable levels of Hg in fine-grained sediment. Because Hg tends to preferentially bind to fine-grained particles, we considered areas with fine-grained substrate to be lower habitat quality compared with areas with coarsergrained substrate, due to the greater possibility for Hg methylization and bioaccumulation. For this reason, we assigned all areas with substrate coarser than coarse sand (1 millimeter [mm]) a substrate suitability score of 100, and areas with bed material finer than 1 mm we assigned a suitability score of 0 (see Exhibit 2). Thus, this substrate criteria is a binary variable every grid cell scores either 0 or 100. We derived the substrate map for the existing condition from field observations and aerial photograph interpretation; we derived the substrate map for the proposed condition from the critical shear-stress calculation for the hydraulic model results for the 2-year (1,450 cfs) flow (see the Yankee Fork Habitat Improvement Projects: Pond Series 2 and Pond Series 3, Hydraulic and Sediment Transport Analyses Technical Memorandum for explanation; [Hydraulic and Sediment Transport Technical Memorandum; CH2M HILL, 2011b in progress]). 2.3 Explanation of Cover Suitability Metric In addition to providing refuge for juvenile Chinook salmon, cover helps to buffer stream temperatures, provide allochthonous materials, and reduce streambank erosion. We considered woody debris, undercut banks, cobble and boulder, aquatic vegetation, large gravel, and overhanging and emergent vegetation all optimal cover. For our analysis, we approximated the part of the water edge that is bordered by overhanging vegetation. To compute the area influenced by edge cover, we assumed that juveniles prefer to remain within 3 feet of the water s edge (Reclamation, 2011). For the existing condition, we mapped the overhanging cover near the edges of the two pond series using aerial photograph interpretation. For the proposed condition, we based the locations of overhanging vegetation on the proposed plans, particularly the areas identified for riparian vegetation enhancement along the pond series (Exhibit 1). We used geographic information system (GIS) and hydraulic model results to create a 3-foot buffer along the covered edge habitat and computed the area of each. 2.4 Combining the Four Suitability Rasters The four habitat suitability rasters were combined to a single habitat-quality raster to look for overall trends and patterns. Maret et al. (2006) recommended using a geometric mean to combine scores for different habitat suitability parameters (i.e., multiplying all the variables and taking the nth root of the product, where n is the number of habitat suitability parameters). Because the cover and substrate variables we used were computed as a binary variables (scores were either 0 or 100), however, many cells score zero on those metrics. In particular, for the cover variable described above, almost all the cells in the raster scored zero except for cells along the water edge in the two pond series. Combining the four suitability scores by multiplying them together leads to a combined score of zero if either cover or substrate is zero. Therefore, we summed the four habitat variables for each cell, resulting in a total habitat suitability score between 0 and What Are the Existing Fish Habitat Conditions in Terms of Quality, Quantity, and Usage? To answer this question, we refer to the existing conditions habitat suitability results. These maps describe fish habitat conditions for the four individual suitability parameters (Exhibits 5 through 9) and for the combined suitability score (Exhibit 10). We provide some initial interpretations of these maps in comment boxes on Exhibits 5 through 9, and they are summarized in Sections 3.1 through 3.5 below. We welcome addition interpretation and input from Reclamation prior to finalization of this draft technical memorandum. COPYRIGHT DECEMBER 23, 2011 BY CH2M HILL, INC. 3

11 HYDRAULIC AND HABITAT SUITABILITY ANALYSES DRAFT TECHNICAL MEMORANDUM 3.1 Velocity Suitability Exhibit 5 shows the existing condition velocity suitability maps and demonstrates, at high resolution, one of the main conclusions of the Draft Yankee Fork Tributary Assessment for the Upper Salmon Subbasin, Custer County, Idaho (Draft Yankee Fork Tributary Assessment; Reclamation, 2011) about this geomorphic reach, YF-2: because the mainstem is relatively steep and confined by narrow valley walls and dredge piles, high velocities throughout the mainstem are not suitable for juvenile Chinook during higher spring flows. Low velocity rearing habitat is a limiting factor in the mainstem. Other than very narrow bands along the edges of the mainstem, off-channel areas are the only areas that are suitable for available for juvenile rearing habitat under existing conditions. Although higher-quality habitat exists in the two pond series under existing condition, these lower-velocity rearing zones are not currently accessible at moderate spring flows. f the four variables analyzed here, velocity is the most important limiting factor for habitat in this reach, especially if a criteria of 2 to 3 fps is considered the maximum usable by juvenile Chinook salmon. 3.2 Depth Suitability Based on the water depth suitability index of Maret et al. (2006) (Exhibit 6), most areas have suitable depths for juvenile salmonids at 650 cfs (dark blue areas). The suitability map based on this criterion (Exhibit 2) shows that the water depth almost everywhere is deeper than 2 feet. As a result, the entire project area (both mainstem as well as pond series) has a habitat score of 100; this pattern is also true for the proposed condition (explained below), with minor changes. The pattern shown in Exhibit 6 mainly reflects using the Maret et al. (2006) depth suitability curve shown in Exhibit 2. If the Raleigh et al. (1986) curve were used to estimate depth suitability, in which suitability decreases with increasing depth greater than 2 feet, then the pattern would be more complex. In that case, the best habitat would be areas around the edges of mainstem and pond series. The mainstem is generally more than 2 feet deep, so using the Raleigh et al. (1986) curve for depth would show impaired habitat quality for this metric in the mainstem. The large, deep ponds provide some areas that generally do not freeze during the winter. Exhibit 7 shows the water depth suitability map using the Raleigh et al. (1986) depth suitability curve, which predicts maximum suitability in water 1- to 2-feet deep and decreasing quality with increasing depth beyond that (Exhibit 4). These maps show poorer habitat in the middle of deep pools (Exhibit 7), reflecting the nonmonotonic shape of Raleigh et al. s (1989) depth suitability curve. In these maps, the highest-quality existing habitat, from the perspective of water depth, is in connecting channels within the pond series. In both cases, appropriate depths exist in both pond series currently; however, these areas are not currently accessible to fish during normal spring snowmelt flows (around 650 cfs). 3.3 Substrate Suitability Exhibit 8 includes the existing condition substrate suitability maps and shows that, from the perspective of substrate suitability, the center of large ponds are impaired as a result of fine-grained substrate. Under existing conditions, the fine-grained substrate in the middle of the ponds provides areas in which Hg uptake and bioaccumulation can occur. The pond series-connecting channels and all of mainstem, where there is mostly gravel, are shown as highquality habitat, according to this metric. The areas in which the substrate suitability are high (coarser substrate) tend to coincide with the areas where velocity suitability are low (high velocities). 4 COPYRIGHT DECEMBER 23, 2011 BY CH2M HILL, INC.

12 3.4 Cover Suitability HYDRAULIC AND HABITAT SUITABILITY ANALYSES DRAFT TECHNICAL MEMORANDUM High-quality cover, defined here as the band within 3 feet of a wetted boundary that has overhanging vegetation, is limited to a few small areas along the fringes of the pond series (Exhibit 9). This parameter does not account for large wood or other cover in the channel or ponds. Edge cover in Exhibit 9 is confined to areas where there is overhanging vegetation along the edge of the pond series. 3.5 Combined Suitability under Existing Conditions We found combining multiple variables representing different types of quantities to be challenging, and potentially misleading. A particularly problematic aspect is combining binary variables (0 or 100) with continuous variables (0 through 100). Nonetheless, we created a combined habitat suitability map by summing the four parameters (Exhibit 10) to see if there are any overall patterns in habitat quality as a combined metric. Using this approach without preferentially weighting variables results in no clear patterns (Exhibit 10). Different parameters of habitat suitability tend to cancel each other out (e.g., where velocities are too high for juveniles, they produce better substrate; depth and cover are also anticorrelated because edges tend to be shallower). So, as a result, the combined suitability map does not provide much useful information, because it predicts relatively similar habitat quality everywhere (Exhibit 10). This pattern conflicts with our field-based understanding of what the existing habitat conditions really are. The velocity habitat condition is the most important limiting factor in this location; therefore, the existing habitat quality is better in both pond series than in the mainstem. This is in contrast to what is shown on the Exhibit 10, which was computed by assuming that all four parameters are of equal value. Differential weighting of parameters is possible, however, this might not be defensible. Adjusting weights would be a subjective process, and therefore, the results could be manipulated to show any expected or desired result. In summary, although it is mathematically possible to compute combined habitat suitability scores, it is more valuable and defensible in this case to look at the different habitat conditions variables individually. 4. What Are the Quantitative Biologic Objectives of Any Proposed Actions? Specific objectives that guided the project design along with their rationale are described in more detail in the Yankee Fork Habitat Improvement Projects: Pond Series 2 and Pond Series 3, Vision, Goals, Objectives, and Design Criteria Technical Memorandum (CH2M HILL, 2011e in progress). Following are the objectives listed in that document, in order of priority: 1. Increase access for juvenile Chinook salmon into and out of each pond series. 2. Increase the quality (complexity, cover, and hydraulic conditions) and quantity of aquatic (juvenile Chinook salmon) and benthic (macroinvertebrate) habitat in both pond series. 3. Improve water quality (temperature and chemistry) in both pond series. 4. Increase the frequency, duration, and volume of flow through both pond series. 5. Increase the quality (diversity) and quantity of riparian and wetland habitat. 6. Improve adult Chinook salmon spawning and holding habitat in the mainstem. Based on these objectives, we developed a set of quantitative criteria that guided the development of the Preliminary (30 Percent) Designs. Following are the quantitative objectives listed in that document (CH2M HILL, 2011e in progress): Route water from the mainstem into each pond series during the time when recently emerged salmonids are seeking high-flow refuge (primarily the overlap of spring runoff with juvenile Chinook salmon emergence [Exhibit 1] typically March to June). COPYRIGHT DECEMBER 23, 2011 BY CH2M HILL, INC. 5

13 HYDRAULIC AND HABITAT SUITABILITY ANALYSES DRAFT TECHNICAL MEMORANDUM Create variable velocities through each pond series both spatially and temporally through the following: Increase velocities in connecting channels and through the center of the large ponds during spring runoff (defined as flows at and above 650 cfs) for two reasons: (1) to flush fine sediment and maintain coarse sediment, which provides interstitial space for macroinvertebrates and cover for juvenile fish and (2) to increase oxygenation of the ponds to reduce Hg methylization Balance this velocity increase with the need to create and maintain low velocity rearing zones (0 to 2.0 fps; Maret et al., 2006) for juvenile Chinook salmon. Create sufficient water depths through the following: Maintain a surface water connection at each outlet at least 0.5 feet deep year-round. Maintain or increase the aerial extent of habitat-appropriate depths (more than 2.0 feet; Maret et al., 2006) in the pond series. Create at least one location in each pond series where the depth is at least 10.0 feet through the winter, for refuge from freezing. Improve the amount of cover and habitat complexity within the pond series; increase large woody debris abundance through each pond series to meet target densities (Riparian Management Objectives criteria of 20 medium to large pieces per mile; Reclamation, 2011); and support recruitment of wood over the long-term. Reduce conditions conducive to methylization of Hg (i.e., low dissolved oxygen, high sulphur concentrations, and high organic carbon and fine sediments), thereby reducing bioaccumulation and biomagnification. Maintain Hg and Se concentrations at levels below those which cause adverse effects to aquatic resources and upper trophic-level consumers (e.g., piscivorous mammals and birds and humans). Maintain water temperatures from greater than 0 degrees Celsius ( C) in winter to approximately 15 C during summer base flows. Temperatures for optimal growth of juvenile Chinook salmon are recognized between 12 and 18 C (Maret et al., 2006). Limit disturbance of dredge tailings to the minimum area and volume necessary to construct the project and focus construction impacts on those areas previously disturbed. 5. Analysis of Project Habitat Impacts 5.1 Explanation Having defined the objectives in a quantitative way and evaluated the hydraulic conditions for the existing condition, we can now evaluate some of the potential habitat-related changes associated with the two pond series projects. Doing this early in the design stage creates opportunities to identify unanticipated negative consequences and, if possible, address them in the later design stages. To keep the discussion and number of figures manageable, we focused on the impacts on Pond Series 3. In general, habitat changes are likely to be similar for both pond series because both comprise large ponds and connecting channels, with inlets that are being engineered to introduce more water at lower flows. While these different geomorphic environments would respond differently from one another within each pond series, both likely would experience a consistent response for similar geomorphic environments. A second reason we focused on Pond Series 3 is because, after the first two iterations of hydraulic modeling (CH2M HILL, 2011a in progress), the suggested inlet design for Pond Series 2 was modified a third time to again increase the volume of flow into Pond Series 2. Therefore, the Pond Series 2 hydraulic modeling results do not represent the Pond Series 2 surface reflected in the Preliminary Design Drawings. For reference, Attachment B includes the results for the habitat suitability analysis for the original Pond Series 2 design. In this discussion, however, we focus the Pond Series 3 impacts, assuming that the project would impact both pond series nearly similarly. 6 COPYRIGHT DECEMBER 23, 2011 BY CH2M HILL, INC.

14 HYDRAULIC AND HABITAT SUITABILITY ANALYSES DRAFT TECHNICAL MEMORANDUM Exhibits 11 through 15 show the Pond Series 3 habitat suitability maps; Panel A on each exhibit computes for the proposed conditions and Panel B computes for the difference between the proposed and existing conditions to quantify any habitat improvement or detriment resulting from the proposed project. 5.2 Interpretation of Results We have noted many of the interpretations in comment boxes on the exhibits themselves, and our initial synthesis interpretation of these results are summarized in the remainder of this section. We welcome addition interpretation and input from Reclamation prior to finalization of this draft technical memorandum Changes in Velocity Suitability Exhibit 11 summarizes the changes in velocity suitability. Increasing flow into Pond Series 3 at 650 cfs would increase water velocities in the pond series, thereby reducing habitat quality scores in the connecting channels, while increasing them in the large ponds (Exhibit 11B). The velocities in the connecting channels, however, would be still low relative to the mainstem (Exhibit 11A), and suitable velocities can still be found on the margins of the connecting channels. Although the velocity increase in connecting channels might result in an incrementally poorer habitat in these areas, overall the proposed project would increase the total amount of velocity-appropriate habitat that can be accessed by juvenile Chinook salmon. For the final design, additional wood or other roughness and complexity elements to the connecting channels could reduce high velocities in these areas and further improve habitat within the connecting channels Changes in Depth Suitability Exhibits 12 and 13 show the depth suitability changes using the Maret et al. (2006) depth suitability curve and Raleigh et al. (1989) curve, respectively. Based on the Maret et al. (2006) assumption (Exhibit 12), in which depths greater than 2 feet are considered the best possible habitat (Exhibit 2), the proposed project would improve the depth-appropriate habitat. The improvements are concentrated around the connecting channel margins, where increasing flow into the pond series from the mainstem would lead to deeper water in the channels, especially around the edges of these features. In addition, a benefit is shown in the marginal areas of the Pond Series 3 large pond because the increased flow into Pond Series 3 would lead to greater pond surface areas, thereby increasing the aerial extent of that pool and its associated habitat. The Raleigh et al. (1989) depth suitability curve (Exhibit 13) assumes the optimal depth for juvenile Chinook salmon is 1 to 2 feet (Exhibit 4), with habitat deteriorating outside of this range. Based on this assumption, the pattern of suitable water depths in Exhibit 13 is more complex than in Exhibit 12. According to the Raleigh et al. (1989) assumption, increasing flow into the pond series would increase flow depths beyond 2 feet in the area around the connecting channels, thus reducing the amount of depth-appropriate habitat in the pond series. We assume the net negative impact on habitat according to the depth variable would be more than offset by gains relative to other measureable variables (e.g., velocity, substrate, and cover), as well as unmeasured ones (e.g., improved access, aeration, and scour for microinvertebrates) Changes in Substrate Suitability Changes in the substrate quality, as measured by the modeled aerial extent of fine-grained (less than 1 mm) bed material that is likely to contain mercury, are shown in Exhibit 14. According to the hydraulic model output, most of the area within Pond Series 3 could mobilize 1-mm and finer sediment during a 2-year (1,450 cfs) flow (Exhibit 14A). In contrast, much of the area within the ponds currently contains fines (Exhibit 8). As a result of introducing more flow into the pond series, we anticipate that substrate conditions in the pond series would improve with little to no effect on the mainstem substrate quality (Exhibit 14B). This improvement within the pond series, however, would reflect the mobilization and transport of fines out of the local system and into the Yankee Fork. The downstream consequences of this are evaluated in the Hydraulic and Sediment Transport Technical Memorandum (CH2M HILL, 2011b in progress). COPYRIGHT DECEMBER 23, 2011 BY CH2M HILL, INC. 7

15 HYDRAULIC AND HABITAT SUITABILITY ANALYSES DRAFT TECHNICAL MEMORANDUM Changes in Cover Suitability Exhibit 9 shows the existing distribution in edge cover, defined here as the zone within 3 feet of the water s edge that also contains overhanging vegetation. Exhibit 15A shows the same for the proposed condition, reflecting plans for riparian vegetation enhancement in the design (Exhibit 1). Exhibit 15B shows areas where such habitat is lost (red) and gained (blue) in Pond Series 3 as a result of the proposed projects. Overall there would be a net gain in edge-cover length and area under the proposed conditions. Exhibit 16 tabulates the difference in the amount of cover area (defined above) in both pond series. Based on the project assumptions and design, Pond Series 3 would gain about 8,000 square feet (ft 2 ) of additional edgecover habitat, and Pond Series 2 would gain an additional 2,000 ft 2, as a result of the planned revegetation program Changes in Combined Habitat Suitability Exhibit 17 contains raster maps showing changes in the sum of the four suitability metrics for the proposed condition (Exhibit 17A) and for the difference between the proposed and existing condition (Exhibit 17B). As discussed previously, combining multiple suitability criteria using the approach described in this technical memorandum, particularly adding binary and continuous variables together and weighting all the variables equally, is problematic and can lead to some misleading conclusions. Considering such, the combined suitability raster map shows overall habitat benefits in the Pond Series 3 and a moderate impairment of habitat in the mainstem; Exhibit 18 summarizes the difference in a table. These combined scores, however, do not represent the actual changes in habitat quality, which can only be ascertained by looking at the individual variables separately and also considering nonmeasured project impacts, such as improved access and water quality. CH2M HILL does not recommend extracting Exhibits 17 and 18 and interpreting them out of context. Interpreting habitat benefits or impacts based only on Exhibits 17 and 18 would be misleading. 6. References Reclamation Draft Yankee Fork Tributary Assessment for the Upper Salmon Subbasin, Custer County, Idaho. United States Department of Interior, Bureau of Reclamation, Pacific Northwest Region 10, Boise, Idaho. September. Maret, T.R., Hortness, J.E., and Ott, D.S Instream Flow Characterization of Upper Salmon River Basin Streams, Central Idaho, U.S. Geological Survey Scientific Investigations Report , 110 pps. CH2M HILL. 2011a in progress. Yankee Fork Habitat Improvement Projects: Pond Series 2 and Pond Series 3, Explanation of Hydraulic Modeling Technical Memorandum. Prepared for United States Department of Interior, Bureau of Reclamation, Pacific Northwest Region 10, Boise, Idaho. CH2M HILL. 2011b in progress. Yankee Fork Habitat Improvement Projects: Pond Series 2 and Pond Series 3, Hydraulic and Sediment Transport Analyses Technical Memorandum. Prepared for United States Department of Interior, Bureau of Reclamation, Pacific Northwest Region 10, Boise, Idaho. CH2M HILL. 2011c in progress. Yankee Fork Habitat Improvement Projects: Pond Series 2 and Pond Series 3, Fisheries Evaluation Technical Memorandum. Prepared for United States Department of Interior, Bureau of Reclamation, Pacific Northwest Region 10, Boise, Idaho. CH2M HILL. 2011d in progress. Yankee Fork Habitat Improvement Projects: Pond Series 2 and Pond Series 3, Geochemical Characterization Technical Memorandum. Prepared for United States Department of Interior, Bureau of Reclamation, Pacific Northwest Region 10, Boise, Idaho. CH2M HILL. 2011e in progress. Yankee Fork Habitat Improvement Projects: Pond Series 2 and Pond Series 3, Vision, Goals, Objectives, and Design Criteria Technical Memorandum. Prepared for United States Department of Interior, Bureau of Reclamation, Pacific Northwest Region 10, Boise, Idaho. 8 COPYRIGHT DECEMBER 23, 2011 BY CH2M HILL, INC.

16 HYDRAULIC AND HABITAT SUITABILITY ANALYSES DRAFT TECHNICAL MEMORANDUM Raleigh, R.F., Miller, W.J., and Nelson, P.C Habitat Suitability Index Model and Instream Flow Suitability Curves Chinook Salmon. Biological Report 82 (10.122). Prepared for the United States Department of the Interior, United States Fish and Wildlife Service, Division of Wildlife and Contaminant Research, National Ecology Center. 64 pps. September. Waddle, T.J PHABSIM for Windows User s Manual and Exercises. United States Geological Survey Open- File Report Prepared for the United States Department of the Interior, United States Geological Survey, Midcontinent Ecological Science Center. 288 pps. November. COPYRIGHT DECEMBER 23, 2011 BY CH2M HILL, INC. 9