Supplemental Analysis_12-16-2016.pdf

Supplemental Information & Analysis for the Sacramento River Bank Protection Project (SRBPP)

Sacramento River Mile 71.3R

December 2016 Revised February 2017

U.S. Army Corps of Engineers Environmental Planning Section

1325 J Street Sacramento, CA 95814-2922

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1 December 2016

1.0 Introduction

The purpose of this document is to provide supplemental information and analysis to support the U.S. Army Corps of Engineers’ (USACE) request for reinitiation of consultation under Section 7 of the Endangered Species Act (16 U.S.C. 1536[c]) for effects of the proposed bank protection action on the right bank of the Sacramento River at River Mile 71.3 (SAC 71.3R) for the Sacramento River Bank Protection Project (SRBPP). The proposed repair at SAC 71.3R was originally described in the Environmental Assessment/Initial Study for Levee Repair of 25 Erosion Sites (hereafter EA, USACE, 2009), and updated to minimize effects to onsite vegetation. This document supplements the EA by providing an updated project description, Standard Assessment Methodology (SAM) analysis for focus fish species (Table 1) green sturgeon, shallow water habitat analysis (Delta smelt), an updated analysis of Essential Fish Habitat (EFH), and an analysis for western yellow-billed cuckoo (Coccyzus americanus americanus). The valley elderberry longhorn beetle (Desmocerus californicus dimorphus) is not expected to be found in the action area. The EA along with supplemental information and analysis, will serve as a BA in USACE’s request for reinitiation of consultation.

1.1 Consultation History

• On October 29, 2007, the US Fish and Wildlife Service (USFWS) received USACE’s October 24, 2007 request for a programmatic formal consultation for the remainder of Phase II of the SRBPP. The request included the final, October 2007, Biological Assessment (Programmatic BA).

• On November 2, 2007, the National Marine Fisheries Service (NMFS) received USACE’s October 24, 2007 request for a programmatic formal consultation for the remainder of Phase II of the SRBPP. The request included the final, October 2007, Biological Assessment (Programmatic BA).

• On June 23, 2008, USFWS issued the Programmatic Biological Opinion (Programmatic BO) for the remaining 24,000 linear feet of authority under the SRBPP, Phase II

(USFWS 2008).

• On July 2, 2008, NMFS issued the Programmatic Biological Opinion (Programmatic BO) for the remaining 24,000 linear feet of authority under the SRBPP, Phase II (NMFS 2008).

• On August 18, 2016, during informal consultation, NMFS and USACE agreed to omit certain species/life stages from the SAM analysis (documented in Table 2).

• On December 27, 2016, the US Fish and Wildlife Service (USFWS) received USACE’s December 22, 2016 request for consultation on the proposed Sacramento River Bank Protection Project at Sacramento River Mile 71.3.

2 December 2016

1.2 Project Description

The erosion repair at SAC 71.3R was initially described in the Environmental Assessment/Initial Study (EA/IS) prepared in 2009 (USACE 2009). The EA/IS proposed implementation of bank protection measures at up to 15,646 linear feet for some of the 25 sites during 2009 and 2010. Ultimately, the levee erosion at SAC 71.3R was not implemented and is now being addressed.

The design for the bank protection action at SAC 71.3R is largely unchanged from the original description in the 25 Sites EA/IS. Changes in quantities of material are the result of updated estimates; the final grade and footprint of the repair is unchanged. The major change to design is that all trees previously identified for removal have been reevaluated and will now be protected in place. A number of trees were originally scheduled for removal on the basis that they had fallen over or were likely to fall as the result of erosion undercutting the roots, and therefore presented a potential risk to the levee or were not compatible with the final repair design. Under reevaluation, USACE determined that it is feasible to protect these trees in place, thereby retaining their existing habitat value. A full project description is included in the 25 sites EA/IS. Table 3 details the old and updated project repair site characteristics for SAC 71.3R.

2.0 Standard Assessment Methodology

The SAM was developed by USACE and Stillwater Sciences, in consultation with NMFS, USFWS, California Department of Fish and Wildlife, and California Department of Water Resources, academic contributions from the University of California at Davis and Humboldt State University, and peer reviewed by sixteen professionals in fish biology, river geomorphology, environmental sciences, and engineering (USACE 2012). The SAM allows agencies to quantitatively assess the potential effects of bank protection and stream restoration projects to ensure that these activities do not jeopardize Chinook salmon, steelhead, and green sturgeon, or destroy or adversely modify their critical habitat. The SAM can also support the determination of suitable compensation for habitat loss by evaluating the benefits of certain design features (e.g., planted emergent vegetation) to focus fish species.

2.1 SAM Modeling Approach

In general, the SAM quantifies habitat values in terms of bankline-weighted or area-weighted species responses. These responses are calculated by combining indices of habitat quality (i.e., fish response indices) with quantity (bank length or wetted-area) for each season, target year, and relevant species/life stage. Recent SAM analyses have simplified the seasonal analysis by consolidating the Summer/Fall (S/F) seasons and the Winter/Spring (W/S) seasons. The SAM employs six habitat variables to characterize near-shore and floodplain habitats of listed fish species:

• Bank slope — average bank slope of each average seasonal water surface elevation;

3 December 2016

• Floodplain availability — ratio of wetted channel and floodplain area during the 2-year flood to the wetted channel area during average winter and spring flows;

• Bank substrate size — the median particle diameter of the bank (i.e., D50) along each average seasonal water surface elevation;

• Instream structure — percent of shoreline coverage of instream woody material along each average seasonal water surface elevation;

• Aquatic vegetation — percent of shoreline coverage of aquatic or riparian vegetation along each average seasonal water surface elevation; and

• Overhanging shade — percent of the shoreline coverage of shade.

The SAM does not directly model changes in the above variables. Instead, habitat changes are estimated separately by the user and entered into an input data file to an Electronic Calculation Template (ECT) developed within a Microsoft Access database to track species responses to project actions over time. Changes in habitat variables may be fixed in time, such as installation of revetment at a particular slope and substrate size. In other circumstances, habitat evolution over time may be represented by more gradual changes in variables such as changes in floodplain inundation due to meander migration or changes in shade due to growth of planted vegetation. Typically, habitat evolution modeling is restricted to shade estimates from riparian growth models, but the SAM accommodates any number of other habitat modeling approaches such as meander migration modeling or large woody Debris recruitment modeling.

Once a particular time series of habitat variable estimates is developed and entered into an

ECT input file, fish responses are calculated using previously developed relationships between habitat variables and species/life stage responses (USACE 2012). The response indices vary from 0 to 1, with 0 representing unsuitable conditions and 1 representing optimal conditions for survival, growth, and/or reproduction. For a given site and scenario (e.g., with-project or without-project), the ECT uses these relationships to determine the responses of individual species and life stages to the measured or predicted values of each variable, for each season and target year. The ECT then multiplies these values together to generate an overall species response index. This index is then multiplied by the linear distance or area of bank to which it applies before the product then generates a weighted species response index (expressed as feet or square feet) in each year of the analysis. The weighted species response index provides a common metric that can be used to quantify habitat values over time, compare project designs to existing conditions, and evaluate the effectiveness of onsite and offsite habitat compensation actions.

2.2 Pre-Project and With-Project Habitat Variable Estimates

This SAM analysis was conducted with the goal of evaluating the response of focus anadromous fish species to the project design updates described above. The pre-project and with-project conditions for this analysis are based on the SAM analysis of 25 sites included in

4 December 2016 the 2009 EA/IS of 25 erosion repair sites. Some pre-project and with-project conditions were modified to be consistent with current application of the SAM model and to reflect the updates to site design. As stated above, the current application of the SAM has been simplified by assuming two key water surface elevations for habitat analysis: S/F and W/S. For the purpose of this analysis, pre-project and with-project values from the existing 25 sites SAM analysis were simplified by adopting fall values for S/F MWSE and winter values for W/S MWSE.

The site-specific timing by year (water year) and season of installed bank protection features, including rock placement, soil and instream woody material installation, and vegetation plantings, were considered in this analysis for the with-project conditions. The pre-project and with-project conditions at SAC 71.3R used in the SAM analyses are presented in Tables 4 and 5.

Descriptions of the habitat variables used in the analysis are discussed below.

2.2.1 Shoreline length

Shoreline length is used as a quantitative attribute by which the qualitative attributes of a site are weighted to achieve a relative response factor. Shoreline lengths at a bank protection site are defined as the total length of continuous shoreline corresponding to each average seasonal flow (USACE 2012). Shoreline lengths were determined by assessing water surface elevations modeled across the breadth of the action area. Pre-project and with-project modeled water surface elevations were used to estimate seasonal shoreline lengths.

2.2.2 Wetted areas

Wetted area is used as a quantitative attribute by which the qualitative attributes of a site are weighted to achieve a relative response factor. Wetted areas at average flow conditions are defined as the wetted channel area of each site (the area between seasonal MWSE and centerline of the river). River centerline was determined through satellite imagery analysis. Seasonal MWSEs were determined by referencing digital elevation models created for each site.

2.2.3 Bank slope

In the SAM, bank slope serves as an indicator of the availability of shallow-water habitat and is obtained from point estimates of bank slope (horizontal change to vertical change, dH:dV) along each seasonal shoreline (i.e., the line where the water surface intersects the bank on average fall, winter, spring, and summer) (USACE 2012). Bank slope for pre-project conditions were derived from the 2009 SAM analysis. The existing bank slope values were originally estimated from onsite survey data or by using GIS software with the topography at each site to determine a bank slope extending from each seasonal shoreline to a depth of approximately 3 ft.

With-project bank slopes were estimated by referencing designs.

2.2.4 Floodplain inundation ratio

In the SAM, floodplain habitat availability is considered important for juvenile life stages and is defined by areas that are flooded by the 2-year flood event (Q2), and measured by calculating a Floodplain Inundation Ratio (USACE 2012). This ratio is calculated by dividing

5 December 2016 the wetted channel and inundated floodplain areas during the 2-year flood event (AQ2) by the wetted channel area (AQavg) during average winter and spring flows. For this analysis, pre-project and with-project values for floodplain inundation ration were derived from the 2009 SAM analysis. The amount of available floodplain habitat is consequently proportional to the ratio’s positive deviation from unity (i.e., values greater than 1). In the absence of a levee setback actions, the amount of available floodplain areas and channel cross sections would not be greatly altered during bank protection activities and thus have minimal impact in a SAM analysis.

2.2.5 Bank Substrate Size

Bank substrate size is directly affected by bank revetment and is considered an important determinant of predation risk and growth for nearly all life stages of the focus fish species (USACE 2012). Therefore, the relevant life stages are positively affected by smaller sizes of bank substrate and negatively affected by larger sizes of bank substrate. For this assessment, bank substrate size represents the median particle size (D50 in inches) within the submerged portion of the bank immediately below (0–3 feet) the seasonal MWSE. The pre-project bank substrate size used in this SAM analysis is consistent with the 2009 SAM value of 0.25 inches for all seasons. Determination of with-project bank substrate size was made by updating values based on changes in design.

2.2.6 Instream Structure

Instream structure is defined as instream woody material (IWM, excluding live bank vegetation) that is partially or fully submerged during average seasonal flows (USACE 2012).

IWM is included in nearly all bank protection designs because it provides hiding and resting cover for focus fish and their predators, in addition to affecting invertebrate food production.

Within the SAM (USACE 2012), bankline cover of IWM along the shorelines is assumed to be proportional to habitat quality for most life stages of the focus fish species. Pre-project and with-project IWM values were determined using site visit estimates along with vegetation planning designs developed by USACE.

2.2.7 Aquatic Vegetation

Aquatic vegetation is defined as aquatic or inundated bank vegetation that is partially or fully submerged during average seasonal flows (USACE 2012). Floating, submerged, and emergent aquatic vegetation serve as hiding cover, and as an invertebrate food production base for both focus fish and their predators. Habitat quality is therefore considered to benefit proportionally with the relative amount of aquatic vegetation along a shoreline. Determination of the cover from aquatic vegetation under with-project conditions was determined by updating values based on changes in design. Aquatic vegetation is not typically planted at the S/F MWSE. Installation of fascine bundles is expected to provide some value to both aquatic vegetation and shade habitat components; however, the successful establishment of fascine bundles at erosion repair sites has varied greatly and cannot be relied upon to contribute to habitat benefits. Aquatic vegetation at W/S MWSE is expected to follow a typical growth model, originally developed by Stillwater Sciences in the 25 sites EA SAM analysis (USACE 2009) and augmented for this SAM analysis

6 December 2016 based on the planting plan cover objectives. Specifically, the objective when designing planting plans for all vegetative cover is 80%; therefore, the expectation of maximum cover for all seasons was modified from 100% to 80%.

2.2.8 Shade

Shade is represented by overhead canopy cover and is measured by estimating the percent of shoreline in which riparian vegetation extends over the water during average seasonal flows.

Overhanging shade is considered to benefit habitat quality by providing hiding cover and food availability for the focus fish species. Values for pre-project shade were derived from the 2009 SAM analysis. Determination of with-project shade cover was made by updating values based on changes in design (protecting all trees in place). Values for shade in winter and spring were modified by 25% and 75% of the existing values, respectively, to incorporate consideration of annual winter defoliation and spring leafing out.

3.0 Biological Simulation and Assessment

Following the procedures outlined in the SAM User’s Manual (USACE 2012), the electronic calculation template (ECT version 4.0) was used to quantify the responses of the focus fish species and life stages to with-project conditions; the ECT uses a 50-year assessment timeline with existing habitat values for each species and life stage described by pre-project conditions.

The SAM model utilizes Water Years (WY) rather than traditional calendar years; SAM WY also differs from traditional hydrologic water years. SAM WY are as follows: Fall (Sept – Nov), Winter (Dec – Feb), Spring (Mar – May), and Summer (Jun – Aug). The ECT was used to calculate a time series of the relative response indices for each pre-project and with-project scenario developed above. Biological responses of each focus fish species life stage were predicted within each habitat unit, and for each time step, based on habitat variable values and fish residency determined from region-specific timing tables (USACE 2012).

In general, as calculated using the ECT, positive differences between the existing and with-project responses are assessed as a net benefit for the focus fish species (i.e., the bank protection action produced superior conditions compared to pre-project conditions). Negative differences indicate the bank protection actions produced inferior conditions when compared with pre-project conditions; they generally require additional habitat compensation.

As stated above, the SAM results provide a basis for determining project effects, and in turn inform the identification of appropriate mitigation. The SAM evaluates the response of focus fish species and their critical life-stages to bank protection measures over a 50 year period of analysis. Results are output as either bankline or wetted area Weighted Response Indices (WRI).

The maximum negative WRI for a juvenile life stage are identified and used as a proxy for offsetting project effects. Although the SAM results are presented as bankline weighted and wetted area weighted WRIs, this analysis will focus on wetted area WRIs because they provide a more relevant representation of project effects than bankline WRIs. Wetted-area weighted results incorporate consideration of loss of wetted area due to construction of project features.

The SAM incorporates the value of onsite mitigative features; therefore, the maximum negative

7 December 2016

WRI should be interpreted as the remaining potential effect that must be mitigated through additional onsite or offsite features, or through the purchase of offsite mitigative credits.

Identifying the maximum negative WRI over the 50 year period of analysis ensures that potential temporal losses are sufficiently considered.

USACE will utilize a reasonable worst-case scenario approach when evaluating the SAM results. This approach errs on the side of caution so that bank protection actions and onsite mitigation are more likely to meet or exceed modeled expectations, while limiting temporal and permanent effects.

4.0 SAM Analysis Results

The SAM is leveraged by USACE, USFWS, and NMFS to inform the determination of appropriate compensation for effects from bank protection actions on listed fish species. The SAM results are not the sole determining factor in the determination of appropriate compensation. It is critical that the SAM analyses be performed and interpreted on a case by case basis. The SAM results for Chinook salmon, steelhead, and green sturgeon are presented in Table 6 and in Figures 1 through 12, and summarized in Table 7. Following is a discussion of the assumptions included in the interpretation of the SAM analysis.

The SAM has been applied in a number of consultations for the SRBPP as well as other projects. The SAM is a flexible model that can inform an effects analysis in varying degrees. In each consultation, the use of the SAM and the interpretation of the SAM has evolved and adapted to other considerations. In recent consultations between USACE and NMFS, interpretation of SAM results has resulted in draft jeopardy opinions. The specific SAM results that resulted in those draft jeopardy opinions were not appropriately interpreted and arguably should have been excluded from the consultation; however, it had been USACE policy to include all default SAM results in consultations. In an effort to provide a clear interpretation of SAM results quantifying potential project effects, results for various species/life-stages have been omitted from this SAM analysis. Results were identified as appropriate for omission and discussed with NMFS during informal consultation. As previously noted, the justification for exclusion of each species/ life stage is provided below and is summarized in Table 2.

Although the SAM quantifies effects for each focus anadromous fish species and their critical life stages at various seasonal conditions, appropriate mitigation was not interpreted as the sum of all SAM predicted maximum negative WRIs. Due to similarities in habitat requirements between species and life stages, and the comprehensive habitat value presented by offsite mitigation banks, mitigation can adequately satisfy effects for multiple species and life stages. The identification of the maximum negative WRI between similar species and life stages was used as a proxy for offsetting project effects to those species.

Results beyond the default life history timing table were excluded for several reasons:

• Life-history timing table is applied at a broad, reach scale and may not be appropriate for a particular repair site. Refinements could include modification of a particular seasonal

8 December 2016 presence or life stage presence, for example a given species/life-stage may not be expected to occur at SAC 71.3R and therefore could be excluded.

• Response not modeled for a particular species/ life-stage. Under default conditions results for species/life-stages not modeled are included in the results. Because response to habitat is not included, those results are ultimately representative of changes in shoreline or wetted area (weighting values) without any consideration of species response. Ultimately, there was not enough information on which to base species response and those results should not be included.

• Response of species/life-stage is not representative of how USACE and NMFS would reasonably expect a species/life-stage to respond to project actions.

4.1 At fall water surface elevation

Reductions in riparian vegetation and placement of rock-revetment along 515 feet of the right bank of the Sacramento River leading to reduced growth and survival of fry and juvenile rearing CV spring-run Chinook salmon, fall-run Chinook salmon, late fall-run Chinook salmon, winter-run Chinook salmon, and CCV steelhead are expected to last at least 50 years after any construction activities associated with the bank repair actions at SAC 71.3R. The amount and extent of this effect is quantified in Table 6. These adverse effects are greatest in Year 6 with a magnitude of -3,475 ft2 WRI for all Chinook runs and -5,693 ft2 for CCV steelhead, and continue for at least 50 years. Short and long term effects from construction of SAC 71.3R to juvenile rearing CV spring-run Chinook salmon, fall-run Chinook salmon, late fall-run Chinook salmon, winter-run Chinook salmon, and CCV steelhead would be adequately offset with the proposed purchase of credits in the amount of 26,097 ft2 from an appropriate mitigation bank.

Reduced growth and survival of juvenile migrating (smolts) CV spring-run Chinook salmon, late fall-run Chinook salmon, winter-run Chinook salmon, and CCV steelhead due to reductions in riparian vegetation and placement of rock-revetment along 515 feet of the right bank of the Sacramento River is expected for at least 50 years after any construction activities associated with the bank repair actions at SAC 71.3R. The amount and extent of this adverse effect is quantified in Table 6. These adverse effects are greatest in Year 7 following construction, with a magnitude of -23,456 ft2 WRI for all Chinook runs and -26,097 ft2 WRI for CCV steelhead, and continue for at least 50 years. With the proposed purchase of credits in the amount of 26,097 ft2 from an appropriate mitigation bank, short and long term effects from the construction of SAC 71.3R to juvenile migrating CV spring-run Chinook salmon, late fall-run Chinook salmon, winter-run Chinook salmon, and CCV steelhead would be adequately offset.

Reduced survival of adult resident CCV steelhead (kelts) is expected for at least 50 years after any construction activities associated with the bank repair actions at SAC 71.3R due to reductions in riparian vegetation along 515 feet of the right bank of the Sacramento River. The amount and extent of this adverse effect is quantified in Table 6. These adverse effects are greatest in Year 6 following construction, with a magnitude of -23,618 ft2 WRI, and continue for at least 50 years. Short and long term effects from the construction of SAC 71.3R to adult

9 December 2016 resident CCV steelhead would be adequately offset with the proposed purchase of credits in the amount of 26,097 ft2 from an appropriate mitigation bank..

Short term reductions in growth and survival for fry and juvenile rearing sDPS green sturgeon are expected for 1 year after any construction activities associated with the bank repair actions at SAC 71.3R due to placement of rock-revetment along 515 feet of the right bank of the Sacramento River. The amount and extent of this adverse effect is quantified in Table 6. These adverse effects begin in Year 1 following construction, with a magnitude of -414 ft2 WRI.

Beneficial effects are expected by Year 2 following construction, and would increase to a magnitude of 10,784 ft2 WRI by Year 50. Short term effects from the construction of SAC 71.3R to fry and juvenile rearing sDPS green sturgeon would be adequately offset with the proposed purchase of credits in the amount of 26,097 ft2 from an appropriate mitigation bank.

4.2 At winter water surface elevations

Improved growth and survival of fry and juvenile rearing CV spring-run Chinook salmon, fall-run Chinook salmon, late fall-run Chinook salmon, winter-run Chinook salmon, and CCV steelhead are expected after any construction activities associated with the bank repair actions at SAC 71.3R due to construction of a riparian bench and installation of IWM along 515 feet of the right bank of the Sacramento River. The amount and extent of this beneficial effect is quantified in Table 6. Beneficial effects are expected immediately following construction, and would increase to a magnitude of 10,795 ft2 WRI for all Chinook runs, and 14,489 ft2 WRI for CCV steelhead, by Year 50.

fall-run Chinook salmon, late fall-run Chinook salmon, and winter-run Chinook salmon is expected for at least 5 years after any construction activities associated with the SAC 71.3R due to reductions in riparian vegetation along 515 feet of the right bank of the Sacramento River.

Reduced growth and survival of juvenile migrating (smolts) CCV steelhead is expected for at least 6 years after any construction activities due to reductions in riparian vegetation along 515 feet of the right bank of the Sacramento River. The amount and extent of this adverse effect is quantified in Table 6. These adverse effects are greatest in Year 1 following construction, with a magnitude of –5,043 ft2 WRI for all Chinook runs and -4,371 ft2 WRI for CCV steelhead.

Beneficial effects are expected by Year 6 for all Chinook runs and Year 7 for CCV steelhead; by Year 50, beneficial effects would increase to a magnitude of 10,317 ft2 WRI and 5,632 ft2 for all Chinook runs and CCV steelhead respectively. With the proposed purchase of credits in the amount of 26,097 square feet from an appropriate mitigation bank, short and long term effects from the construction of SAC 71.3R to juvenile migrating CV spring-run Chinook salmon, fall-run Chinook salmon, late fall-run Chinook salmon, winter-run Chinook salmon, and CCV steelhead would be adequately offset.

after any construction activities associated with the bank repair actions at SAC 71.3R due to reductions in riparian vegetation along 515 feet of the right bank of the Sacramento River. The amount and extent of this adverse effect is quantified in Table 6. These adverse effects are greatest in Year 2 following construction with a magnitude of -7,339 ft2 WRI, and continue for at

10 December 2016 least 50 years. With the proposed purchase of credits in the amount of 26,097 ft2 from an appropriate mitigation bank, short and long term effects from the construction of SAC 71.3R to adult resident CCV steelhead would be adequately offset.

Improved growth and survival of fry and juvenile rearing sDPS green sturgeon is expected after any construction activities associated with SAC 71.3R due to construction of a riparian bench and installation of IWM along 515 feet of the right bank of the Sacramento River.

Beneficial effects are expected immediately following construction, and would increase to a magnitude of 12,742 ft2 for sDPS green sturgeon by Year 50. The amount and extent of this beneficial effect is quantified in Table 6.

4.3 At spring water surface elevations

Improved growth and survival of fry and juvenile rearing CV spring-run Chinook salmon, fall-run Chinook salmon, late fall-run Chinook salmon, winter-run Chinook salmon, and CCV steelhead are expected after any construction activities associated with SAC 71.3R due to construction of a riparian bench and installation of IWM along 515 feet of the right bank of the Sacramento River. The amount and extent of this beneficial effect is quantified in Table 6.

Beneficial effects are expected immediately following construction, and would increase to a magnitude of 15,120 ft2 WRI for all Chinook runs, and 18,705 ft2 WRI for CCV steelhead, by Year 50.

Reduced growth and survival of juvenile migrating (smolts) CV spring-run Chinook salmon and winter-run Chinook salmon are expected for at least 3 years after any construction activities associated with the SAC 71.3R due to reductions in riparian vegetation along 515 feet of the right bank of the Sacramento River. Reduced growth and survival of juvenile migrating (smolts) CCV steelhead is expected for at least 5 years after any construction activities associated with the SAC 71.3R due to reductions in riparian vegetation along 515 feet of the right bank of the Sacramento River. These adverse effects are greatest in Year 1 following construction, with a magnitude of –3,598 ft2 WRI for all Chinook runs and -4,732 ft2 WRI for CCV steelhead. The amount and extent of these adverse effects is quantified in Table 6. For CCV steelhead, beneficial effects are expected by Year 6, and by Year 50 would increase to a magnitude of 6,046 ft2 WRI. For Chinook runs, beneficial effects are expected by Year 4, and by Year 50 would increase to a magnitude of 11,177 ft2 WRI. With the proposed purchase of credits in the amount of 26,097 ft2 from an appropriate mitigation bank, short and long term effects from the construction of SAC 71.3R to juvenile migrating CV spring-run Chinook salmon, winter-run Chinook salmon, and CCV steelhead would be adequately offset.

after any construction activities associated with bank repair actions at SAC 71.3R due to reductions in riparian vegetation along 515 feet of the right bank of the Sacramento River. The amount and extent of this adverse effect is quantified in Table 6. These adverse effects are greatest in Year 2 following construction, with a magnitude of -10,037 ft2 WRI, and continue for at least 50 years. With the proposed purchase of credits in the amount of 26,097 ft2 from an adult resident CCV steelhead would be adequately offset.

11 December 2016 bench and installation of IWM along 515 feet of the right bank of the Sacramento River.

Beneficial effects are expected immediately following construction, and would increase to a magnitude of 12,742 ft2 for sDPS green sturgeon by Year 50. The amount and extent of this beneficial effect is quantified in Table 6.

4.4 At summer water surface elevations

Reduced growth and survival of fry and juvenile rearing CV spring-run Chinook salmon, fall-run Chinook salmon, late fall-run Chinook salmon, winter-run Chinook salmon, and CCV steelhead are expected to last at least 50 years after any construction activities associated with bank repair actions at SAC 71.3R due to reductions in riparian vegetation and placement of rock-revetment along 515 feet of the right bank of the Sacramento River. The amount and extent of this effect is quantified in Table 6. These adverse effects are greatest in Year 1, with a magnitude of -3,744 ft2 WRI for all Chinook runs, and -6,105 ft2 for CCV steelhead, and are expected to last for at least 50 years. Short and long term effects from construction of SAC 71.3R to juvenile rearing CV spring-run Chinook salmon, fall-run Chinook salmon, late fall-run Chinook salmon, winter-run Chinook salmon, and CCV steelhead would be adequately offset with the proposed purchase of credits in the amount of 26,097 ft2 from an appropriate mitigation bank.

is expected for at least 50 years after any construction activities associated with bank repair actions at SAC 71.3R due to reductions in riparian vegetation and placement of rock-revetment along 515 feet of the right bank of the Sacramento River. The amount and extent of this adverse effect is quantified in Table 6. This adverse effect is greatest in Year 1 following construction, with a magnitude of -24,879 ft2 WRI for CV spring-run Chinook salmon, and continue for at least 50 years. With the proposed purchase of credits in the amount of 26,097 ft2 from an juvenile migrating CV spring-run Chinook salmon would be adequately offset.

Reduced survival of adult resident CCV steelhead (kelts) in expected for at least 50 years after any construction activities associated with bank repair actions at SAC 71.3R due to reductions in riparian vegetation along 515 feet of the right bank of the Sacramento River. The amount and extent of this adverse effect is quantified in Table 6. These adverse effects are greatest in Year 1 following construction, with a magnitude of -24,262 ft2 WRI, and continue for at least 50 years. Short and long term effects from the construction of SAC 71.3R to adult resident CCV steelhead would be adequately offset with the proposed purchase of credits in the amount of 26,097 ft2 from an appropriate mitigation bank.

bench and installation of IWM along 515 feet of the right bank of the Sacramento River. The amount and extent of this beneficial effect is quantified in Table 6. Beneficial effects are

12 December 2016 expected immediately following construction, and would increase to a magnitude of 11,013 ft2 for sDPS green sturgeon by Year 50.

5.0 Supplemental Green Sturgeon Analysis

Through informal consultation with the resource agencies, NMFS identified additional concerns regarding potential impacts to green sturgeon that were not adequately evaluated through the SAM analysis. The SAM is somewhat limited in its ability to predict a complete range of potential project impacts on all focus fish species and life stages, as the SAM is focused primarily on changes to nearshore/bank habitat. The SAM does not adequately assess potential impacts to deeper benthic habitat. NMFS identified the placement of rock revetment over natural bank substrate as a potential impact to adult green sturgeon life stages. In past consultations, USACE has recognized the potential for impacts to benthic oriented species/life stages, including green sturgeon, from the placement of rock revetment; however, the nature of the impact to benthic habitat and the use of that habitat by focus fish species is difficult to define on a system wide or site specific scale. This section will provide additional analysis to address the potential impact to green sturgeon due to the placement of rock revetment over native benthic substrate at SAC 71.3R. Specifically this analysis will evaluate the potential effects of the placement of rock revetment over native substrate on the Primary Constituent Elements (PCEs) of green sturgeon habitat (NMFS 2009) at SAC 71.3R.

Characterization of existing benthic conditions

USACE collected additional information to characterize the existing benthic conditions at SAC 71.3 to help better understand potential effects from the proposed project action. This additional information included an evaluation of existing hydraulic conditions using the adaptive hydraulics model (AdH) that was built to evaluate the existing and alternative conditions for environmental analysis. USACE also conducted a field survey of the existing benthic conditions within the footprint of the project site and adjacent areas to characterize changes resulting from project actions.

The AdH model was used to extract depths and velocities at SAC 71.3R at representative flows of 10k, 16k, and 23k cfs (Figures 13 and 14). The selected flows represent approximately 80%, 50%, and 20% probability of exceedance of 10k, 16k, and 23k cfs respectively for the period of time that green sturgeon are expected to occur at the site (March – August). Across the range of representative flows, velocities within the project footprint averaged between 0.3 and

0.6 m/s and reached maximum values from 0.5 to 0.9 m/s (Figure 13). Depths within the project footprint averaged between 3.4 – 4.9 m and reached maximum values from 5.3 to 8.3 m. In general, the channel at SAC 71.3R is relatively uniform, with sloping sides, a flat bottom, and high water velocities.

The benthic survey was conducted to determine substrate conditions and biological community assemblage within the project footprint and a nearby previously constructed site to help determine resultant changes from the proposed action. On 9/28/2016 and 9/29/2016, benthic samples were collected onsite and at adjacent locations using a ponar grab sampler. The sampling plan included collection of benthic grab samples from 62 locations in triplicate; 21

13 December 2016 locations within the project footprint and another 10 locations extending across the channel in two transects (Figure 14). Two other sites were also sampled, one just upstream of SAC 71.3R and another at a previous repair with a bench similar to the proposed design at SAC 71.3R.

These sites were sampled both along the right bank, and along two cross-channel transects.

The grab samples collected within the project footprint and at most of the right bank locations yielded almost no soft substrate material, but occasionally consisted of clay chunks and a few pieces of gravel. This is consistent with observations of a dominant hardpan substrate along the shoreline. As samples were collected across the channel, sand and gravel was observed, indicating the right bank channel is mostly scoured of sediments while the left channel retained some sand and gravel.

The benthic sampling yielded highly variable biological results. Sampling along the right bank yielded high densities of loose clams at times, but not consistently. Even in the replicate sampling, often observed was 2 samples with no organisms or substrate, and the third consisting of high numbers of clams with no substrate. Overall, invertebrates were identified at 57% of the locations within the project footprint, and at 66% of the locations outside of the project footprint.

The number of invertebrates collected at each location ranged from 0 – 50 and were highly variable even in the replicate samples. All collected invertebrates were of the same species, Corbicula fluminea; an exotic clam. The absence of soft substrate at the project site and along the right side of the channel along this reach suggest that there is no biological productivity occurring due to the inability of organisms to establish. The presence of clams in these samples are likely the result of erosive actions upstream that deposit clams into the high velocity portion of the river bottom.

The consideration of the benthic sampling results along with the hydraulic information collected in this reach suggests the river conditions within this reach are very dynamic. Soft substrates are largely absent or transitional, except along the left bank, opposite from the SAC 71.3R project site. For these reasons, the project site is likely not very supportive of biological production in the benthos.

Food resources

The green sturgeon PCEs for food resources identifies the need for abundant food items for larval, juvenile, sub-adult, and adult life stages. In the designation of critical habitat for green sturgeon, NMFS indicates that juvenile green sturgeon within freshwater riverine systems most likely feed on amphipods, bivalves, and fly larvae (NMFS, 2009). It is uncertain whether adult green sturgeon feed in freshwater systems during or immediately after spawning; however, if sub-adult and adult green sturgeon feed in freshwater rivers, then they most likely feed on benthic prey species similar to those fed on in bays and estuaries, including shrimp, clams, and benthic fish (Moyle et al. 1995; Erickson et al. 2002; Moser and Lindley 2007; Dumbauld et al.

2008).

Although invertebrates were observed onsite, the lack of soft bottom substrates, relative high velocities, and uniform channel bathymetry, suggest that the river in the project reach is flushed clean of sediment and is not likely providing significant production of green sturgeon forage items. The condition of the invertebrates collected during sampling suggests that the clams are

14 December 2016 likely being transported along the bottom along with lose substrate and debris. Placement of rock revetment would not inhibit the natural transport of materials downstream.

Substrate type or size

The green sturgeon PCEs for substrate type or size primarily identifies a need for substrates suitable for egg deposition and development (e.g., bedrock sills and shelves, boulder, or cobble and gravel, with interstices or irregular surfaces to “collect” eggs and provide protection from predators, and free of excessive silt and debris that could smother eggs during incubation), larval development (e.g., substrates with interstices or voids providing refuge from predators and from high flow conditions), and sub-adults and adults (e.g., substrates for holding and spawning)

(NMFS 2009).

Spawning has not been documented in the reach of the river near SAC 71.3R and, therefore, no adverse effects are expected to green sturgeon spawning from the proposed bank protection measures. The potential effect of substrate to support larval and juvenile rearing is captured in the SAM analysis, and will not be discussed further here. Substrate type or size could be important for adult and sub-adult green sturgeon with regards to supporting spawning, holding, or foraging behavior; however, due to a lack of suitable spawning and holding habitat, or production of forage items onsite, a change in substrate would not impact those behaviors.

Juvenile green sturgeon migrants have been observed to exhibit nocturnal behavior, hiding in rocks during daytime (Kynard 2005); therefore, placed rock can provide complexity and hydraulic refuge, in which case the proposed bank protection measures at SAC 71.3R could provide some value compared to the existing conditions in this reach.

Depth

The green sturgeon PCEs for depth identifies a need for deep (≥ 5 m) pools for both upstream and downstream holding of adult or sub-adult fish, with adequate water quality and flow to maintain the physiological needs of the holding adult or sub-adult fish (NMFS, 2009). Deep pools of ≥ 5 m depth, with complex hydraulic features and upwelling, are critical for adult green sturgeon spawning and for summer holding within the Sacramento River (Vogel 2008; Poytress et al. 2009).

While existing conditions at SAC 71.3R do include depths greater than 5m at certain flows, the analysis of bathymetry and velocity does not indicate the presence of any pools. Placement of rock revetment at SAC 71.3R will not alter the depth in a manner that would affect the normal use of the river reach by adult or sub-adult green sturgeon.

In summary, while USACE continues to recognize the potential for placement of rock revetment to affect listed fish species, placement of rock revetment at SAC 71.3R would not likely adversely affect any of the critical habitat elements that support the natural behavior of green sturgeon.

15 December 2016

6.0 Shallow Water Habitat Analysis Results

The proposed bank protection action at SAC 71.3R is not located within designated critical habitat for Delta smelt; however, Delta smelt have been observed in the vicinity and therefore USACE has included an analysis of potential effects to habitat. In accordance with recommendations from USFWS, the SAM is no longer used in the assessment of project effects to Delta smelt and their habitat. USACE has adopted an alternative method (in coordination with USFWS) for quantifying effects to Delta smelt that evaluates changes in shallow water habitat.

Shallow water habitat is used as a measure of habitat critical for the spawning life stage of Delta smelt, and may also provide a role in adult migration. USFWS has defined shallow water habitat as all waters between Mean High Water (MHW) and 3 meters below Mean Lower Low Water (MLLW)(USFWS 2004). MHW was calculated as 13 feet and the MLLW was calculated as 12ft (NAVD88). For the purpose of this analysis shallow water habitat was evaluated as the area between MLLW (13ft) and 3m below MLLW (2ft). Project footprint was used to define upstream and downstream boundaries.

A desktop analysis was performed to evaluate the change in shallow water habitat. Two types of effects on shallow water were evaluated. The first type of effect evaluated was the change in available shallow water habitat as defined above. The second type of effect evaluated was the wetted area permanently lost due to construction of riparian bench, measured as the area between pre-project MHW and with-project MHW.

The bank protection action at SAC 71.3R would result in long term effects for Delta smelt, including permanent loss of 11,867 ft2 (0.27 acres) of wetted area due to placement of rock revetment and a slight permanent increase of 257 ft2 (0.005 acres) of shallow water habitat due to change in slope. For the purpose of quantifying effects to shallow water habitat, the slight permanent increase in shallow water will not be included further.

In addition to the evaluation of shallow water habitat, consideration was given to potential adverse effects from the placement of rock revetment. In designating critical habitat for the Delta smelt, USFWS identified four PCEs essential to the conservation of the species. Bank protection actions at SAC 71.3R have the potential to effect PCE#1: Physical Habitat, which is defined as the structural components of a habitat. Specifically, adverse effects to shallow water habitat could occur through changes in substrate as the result of the placement of rock revetment.

This modification only has the potential to affect the spawning life stage of Delta smelt. The general effects of sediment on habitat as it pertains to other life stages of Delta smelt has been analyzed and would suggest that Delta smelt do not exhibit particularly strong substrate preferences. Spawning Delta smelt are thought to require sandy or small gravel substrates for egg deposition. With-project conditions will modify substrate in 2 distinct areas. Area above the S/F MWSE, will be a planted riparian bench with natural substrate and will not adversely affect the physical habitat (PCE#1) component of Delta smelt. Area below the S/F MWSE will be uncovered rock revetment and will represent a permanent change in substrate. The area of substrate permanently affected by the placement of rock revetment is 8,794 ft2 (0.20 acres).

Natural sediment (silt/sand/clay) aggradation and degradation has been observed to accumulate following placement of rock revetment at SRBPP repair sites; however, the

16 December 2016 composition of that substrate and the timing of the aggradation/degradation has not been documented. Due to natural patterns of aggradation and degradation, it is possible that the placement of rock revetment does not result in a permanent loss of habitat value with regards to available substrate, therefore, the extent of the effect that the change of substrate below S/F MWSE will have on Delta smelt is not entirely clear. Although available information does not provide a complete understanding of the relative reduction in quality of Delta smelt spawning habitat due to placement of rock revetment, USACE recognizes the critical status of the species and the importance of compensating for any potential adverse effects. Therefore, USACE will include conversion of 0.20 acres of natural substrate to rock revetment in our final accounting of adverse effects to Delta smelt habitat, for a total of 0.47 acres (Table 8).

7.0 Western Yellow Billed Cuckoo Effects Analysis

The western yellow-billed cuckoo was not a Federally-listed species at the time the 25 sites EA/IS was written and consequently no effects analysis was completed. The following information will support USACE’s determination of no effect.

7.1 Status of the species

7.1.1 Status and Distribution

In 2001, USFWS determined that there was sufficient evidence to list the western yellow-billed cuckoo but was precluded by higher priority listing actions and that the threat to the species was determined to…