NMFS-BiOp.pdf

TABLE OF CONTENTS

1. INTRODUCTION

1.1 Background

1.2 Consultation History

1.3 Proposed Federal Action

1.3.1 Interrelated and Interdependent Actions

2. ENDANGERED SPECIES ACT:

2.1 Analytical Approach

2.1.1 Use of Analytical Surrogates

2.2 Rangewide Status of the Species and Critical Habitat

2.2.1 California Central Valley Spring-run Chinook salmon

2.2.2 California Central Valley Steelhead

2.2.3 Sacramento River Winter-run Chinook Salmon

2.2.4 Southern Distinct Population Segment (sDPS) of North American Green Sturgeon

2.2.5 Global Climate Change

2.3 Action Area

2.4 Environmental Baseline

2.5 Effects of the Action

2.5.1 Construction Impact Analysis for Salmonids and Green Sturgeon

2.5.2 Project Effects on Salmonids, Estimated Using Standard Assessment Methodology as an

Analytical Surrogate

2.5.3 Project Effects to sDPS Green Sturgeon, Estimated Using Habitat Loss as an Analytical

Surrogates

2.5.4 Project Effects on Critical Habitat

2.6 Cumulative Effects

2.6.1 Agricultural Practices

2.6.2 Aquaculture and Fish Hatcheries

2.6.3 Increased Urbanization

2.6.4 Rock Revetment and Levee Repair Projects

2.7 Integration and Synthesis

2.7.1 Status of the Sacramento River Winter-Run Chinook Salmon ESU

2.7.2 Status of the CV Spring-Run Chinook Salmon ESU

2.7.3 Status of the CCV Steelhead DPS

2.7.4 Status of the Green Sturgeon southern DPS

2.7.5 Status of the Environmental Baseline and Cumulative Effects in the Action Area

2.7.6 Summary of Project Effects on Sacramento River Winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead and sDPS Green Sturgeon Individuals

2.7.7 Summary of Project Effects on Sacramento River Winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead and sDPS Green Sturgeon Critical Habitat

2.7.8 Summary

2.8 Conclusion

2.9 Incidental Take Statement

2.9.1 Amount or Extent of Take

2.9.2 Effect of the Take

2.9.3 Reasonable and Prudent Measures

2.9.4 Terms and Conditions

2.10 Conservation Recommendations

2.11 Reinitiation of Consultation

3. MAGNUSON-STEVENS FISHERY CONSERVATION AND MANAGEMENT ACT

ESSENTIAL FISH HABITAT RESPONSE

3.1 Essential Fish Habitat Affected by the Project

3.2 Adverse Effects on Essential Fish Habitat

3.3 Supplemental Consultation

4. DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION

REVIEW

4.1 Utility

4.2 Integrity

4.3 Objectivity

5. REFERENCES

1. INTRODUCTION

This Introduction section provides information relevant to the other sections of this document and is incorporated by reference into Sections 2 and 3 below.

1.1 Background

The National Marine Fisheries Service (NMFS) prepared the biological opinion (BO) and incidental take statement (ITS) portions of this document in accordance with section 7(b) of the

Endangered Species Act (ESA) of 1973 (16 USC 1531 et seq.), and implementing regulations at

50 CFR 402.

We also completed an essential fish habitat (EFH) consultation on the Proposed Action, in accordance with section 305(b)(2) of the Magnuson-Stevens Fishery Conservation and

Management Act (MSA) (16 U.S.C. 1801 et seq.) and implementing regulations at 50 CFR 600.

We completed pre-dissemination review of this document using standards for utility, integrity, and objectivity in compliance with applicable guidelines issued under the Data Quality Act

(DQA) (section 515 of the Treasury and General Government Appropriations Act for Fiscal Year

2001, Public Law 106-554). The document will be available through NMFS’ Public Consultation

Tracking System https://pcts.nmfs.noaa.gov/pcts-web/homepage.pcts. A complete record of this consultation is on file at the NMFS California Central Valley Area Office.

1.2 Consultation History

On November 2, 2007, NMFS received a formal consultation request from the U.S. Army Corps of Engineers (USACE) for Phase II of the Sacramento River Bank Protection Project (SRBPP).

In response, NMFS issued a programmatic BO for this project on July 02, 2008. The programmatic BO requires subsequent formal consultations for site specific projects developed under the Phase II authority for SRBPP.

On August 18, September 14, and October 20, 2016, NMFS and the USACE held preconsultation technical meetings regarding work to be completed as part of the above programmatic consultation at river mile (RM) 71.3 on the Sacramento River.

On January 12 2017, the USACE sent a letter requesting initiation of formal consultation for this work at RM 71.3, hereafter referred to as SRBPP RM 71.3. This letter was accompanied by a

Draft Environmental Assessment/Initial Study for Levee Repair of 25 Erosion Sites, a Final

Environmental Assessment/Initial Study for Levee Repair of 25 Erosion Sites, and a

Supplemental Information and Analysis for the SRBPP.

NMFS requested more information about the project on January 18, 2017 and February 10, 2017.

NMFS received this information and initiated consultation on February 17, 2017. A complete administrative record is on file at the NMFS Central Valley Area Office in Sacramento, California.

1.3 Proposed Federal Action

“Action” means all activities or programs of any kind authorized, funded, or carried out, in whole or in part, by Federal agencies (50 CFR 402.02). USACE and the Central Valley Flood

Protection Board (CVFPB) propose to implement bank protection measures on the Sacramento

River at river mile (RM) 71.3, located near the Sacramento International Airport in Yolo County, California.

The levee erosion at site RM 71.3 is likely due to high-velocity flood flows, boat wake wave impacts, and erodible levee materials. Figures 1 and 2 below shows a cross section of the repair, which will be 515 feet long. The upper bench (at A – B on Figure 1), will have a rock slope of

2.5H:1V (horizontal to vertical ratio), and the lower bench (at B – C on Figure 1) will have a slope of 10H:1V. The upper and lower bench will be covered in a total of 33,837 ft2 of soil-filled quarry stone, with a 0.5 foot of soil cover on top to support riparian plantings. A mix of trees, willows, and native understory/grasses will be planted on both the upper and lower slope of the riparian bench. The species to be planted and the specific zones they will be planted in is described in Figure 2 and Table 2. A beaver barrier fence (at C on Figure 1) will be installed immediately below the riparian plantings in order to protect them from beaver predation. The riverside edge of the bench will be set at the summer mean water surface elevation (SMWSE).

Just below the lower bench, a rock toe will be installed with a 2:1 slope using 13,684 ft2 of quarry stone (at C – D on Figure 1), which will remain bare. Table 1 describes the repair site characteristics.

Table 1. Repair Site Characteristics

Repair Site Characteristics Value

Length of Repair Site (feet) 515

Site Area (acres) 4.48

Quarry stone volume (cubic yards) 7,934

Soil-filled quarry stone volume (cubic yards) 4,700

Soil cover volume (cubic yards) 727

Final bank slope outside of planted bench area (H:V) 2.5:1

Final slope within riparian bench (H:V) 10:1

Instream Woody Material to be removed (linear feet along bank) 123

Instream Woody Material to be anchored at MSWL (linear feet) 257.5

The USACE plans to mitigate for project impacts to salmon and steelhead by purchasing credits from an approved mitigation bank at a 1:1 ratio. Specifically, a total of 0.60 acres (26,079 ft2) of credits will be purchased, which represents the maximum negative weighted response index value (WRI) estimated by the standard assessment methodology (SAM) analysis. This analysis is described below in the Analytical Approach and Effects of the Action sections.

No trees will be removed for the proposed project. Although a total of 123 linear feet of instream woody material (IWM) will need to be removed to facilitate the repair of the bank, 257.5 linear feet of IWM will be installed as mitigation. The IWM will be installed at SMWSE in grouping spaced 20-25 feet apart with one end buried in the quarry stone to anchor it. In-water construction will be limited to between July 1 and November 30. A complete description of avoidance and mitigation measures for the proposed project can be found in the Sacramento

River Bank Protection Project Phase II programmatic BO, issued on July 02, 2008.

In an effort to improve the evaluation of impacts to green sturgeon from bank protection actions, USACE will conduct pre and post construction monitoring to monitor changes to benthic form and function. The goals of the monitoring will be to establish an understanding of existing benthic form and communities within the project reach, explore and develop monitoring techniques, and provide information for future monitoring. Monitoring will be conducted upstream, downstream, and at RM 71.3. Pre and post construction monitoring will occur at a minimum once quarterly, but may be conducted as often as once per month if relevant to achieving the goals stated above. Post-construction monitoring would continue for at least 5 years, but may be continued up to 10 years. USACE anticipates that long term monitoring conducted in conjunction with construction of the bank protection action at RM 71.3 will be superseded by more comprehensive monitoring efforts. Monitoring results will be reported to

NMFS at a minimum once per year, or as appropriate. In addition, USACE will coordinate regularly with NMFS through the Interagency Working Group to ensure that monitoring continues to meet the stated goals above.

1.3.1 Interrelated and Interdependent Actions

“Interrelated actions” are those that are part of a larger action and depend on the larger action for their justification. “Interdependent actions” are those that have no independent utility apart from the action under consideration (50 CFR 402.02). There are no interdependent or interrelated activities associated with the proposed action.

Figure 1. Cross section of the bank repair for the Sacramento River Bank Protection Project work to be completed at river mile 71.3 of the Sacramento River

Figure 2. Cross section of the bank repair for the Sacramento River Bank Protection Project work to be completed at river mile 71.3 of the Sacramento River

Table 2. Riparian planting palette

Planting Zone

Area of Planting

Zone

(sq. ft)

Area of Planting Zone (ac)

Notes Species Name Common Name

Zone 1 20,977 0.48

Zone 1A Overstory

Quercus lobata Valley oak

Quercus wislizeni Interior live oak

Artemisia douglasiana California mugwort

Baccharis salicifolia mule fat

Zone 1A- Understory Hydroseed

Mix

Achillea millefolium yarrow

Elymus glaucus blue wildrye

Hordeum brachyantherum ssp. californicum

California barley

Leymus triticoides creeping wild rye

Leymus triticoides creeping wild rye

Lotus purshianus var.

purshianus

Spanish clover

Lupinus bicolor miniature lupine

Nasella pulchra purple needle grass

Trifolium wildenovii tomcat clover

Vulpia microstachys small fescue

Zone

Area of Planting

Zone

(sq. ft)

Area of Planting Zone (ac)

Notes Species Name Common Name

Zone 2 20,263 0.47

Zone 2 Over & Middle

Story

Acer negundo Box elder

Alnus rhombifolia White Alder

Cephalanthus occidentalis Buttonbush

Fraxinus latifolia Oregon ash

Populus fremonitii ssp.

Fremonitii

Fremont cottonwood

Quercus lobata Valley oak

Zone 2 grasses

Agrostis exarta spike bentgrass

Ambrosia psilostachya western ragweed

Artemisia douglasiana California mugwort

Carex barbarae Santa Barbara carex

Deschampsia elongata slender hairgrass

Elymus trachycaulus slender wheatgrass

Hordeum brachyantherum ssp. californicum

California barley

Juncus Balticus Baltic rush

Juncus Effusus Common rush

Leymus triticoides creeping wild rye

Zone

Area of Planting

Zone

(sq. ft)

Area of Planting Zone (ac)

Notes Species Name Common Name

Zone 3 20,263 0.47

Zone 3 Over & Middle

Story

Acer negundo Box elder

Alnus rhombifolia White Alder

Cephalanthus occidentalis Buttonbush

Fraxinus latifolia Oregon ash

Populus fremonitii ssp.

Fremonitii

Fremont cottonwood

Salix exigua Sandbar willow

Salix lasiolepii Arroyo willow

Zone 3 grasses

Agrostis exarta spike bentgrass

Ambrosia psilostachya western ragweed

Artemisia douglasiana California mugwort

Carex barbarae Santa Barbara carex

Deschampsia elongata slender hairgrass

Elymus trachycaulus slender wheatgrass

Hordeum brachyantherum ssp. californicum

California barley

Juncus Balticus Baltic rush

Juncus Effusus Common rush

Leymus triticoides creeping wild rye

Fascine Bundles

Salix exigua Sandbar willow

2. ENDANGERED SPECIES ACT:

BIOLOGICAL OPINION AND INCIDENTAL TAKE STATEMENT

The ESA establishes a national program for conserving threatened and endangered species of fish, wildlife, plants, and the habitat upon which they depend. As required by section 7(a)(2) of the ESA, each Federal agency must ensure that its actions are not likely to jeopardize the continued existence of endangered or threatened species, or adversely modify or destroy their designated critical habitat. Per the requirements of the ESA, Federal action agencies consult with

NMFS and section 7(b)(3) requires that, at the conclusion of consultation, NMFS provides an opinion stating how the agency’s actions would affect listed species and their critical habitats. If incidental take is reasonably certain to occur, section 7(b)(4) requires NMFS to provide an ITS that specifies the impact of any incidental taking and includes non-discretionary reasonable and prudent measures (RPMs) and terms and conditions to minimize such impacts.

2.1 Analytical Approach

This BO includes both a jeopardy analysis and/or an adverse modification analysis. The jeopardy analysis relies upon the regulatory definition of “to jeopardize the continued existence of” a listed species, which is “to engage in an action that would be expected, directly or indirectly, to reduce appreciably the likelihood of both the survival and recovery of a listed species in the wild by reducing the reproduction, numbers, or distribution of that species” (50 CFR 402.02).

Therefore, the jeopardy analysis considers both survival and recovery of the species.

This BO relies on the definition of "destruction or adverse modification," which “means a direct or indirect alteration that appreciably diminishes the value of critical habitat for the conservation of a listed species. Such alterations may include, but are not limited to, those that alter the physical or biological features essential to the conservation of a species or that preclude or significantly delay development of such features” (81 FR 7214).

The designation(s) of critical habitat for (species) use(s) the term primary constituent element

(PCE) or essential features. The new critical habitat regulations (81 FR 7414) replace this term with physical or biological features (PBFs). The shift in terminology does not change the approach used in conducting a ‘‘destruction or adverse modification’’ analysis, which is the same regardless of whether the original designation identified PCEs, PBFs, or essential features.

In this BO, we use the term PBF to mean PCE or essential feature, as appropriate for the specific critical habitat.

We use the following approach to determine whether a Proposed Action is likely to jeopardize listed species or destroy or adversely modify critical habitat:

1. Identify the rangewide status of the species and critical habitat expected to be adversely affected by the Proposed Action.

2. Describe the environmental baseline in the Action Area.

3. Analyze the effects of the Proposed Action on both species and their habitat using an

“exposure-response-risk” approach.

4. Describe any cumulative effects in the Action Area.

5. Integrate and synthesize the above factors by: (1) Reviewing the status of the species and critical habitat; and (2) adding the effects of the action, the environmental baseline, and cumulative effects to assess the risk that the Proposed Action poses to species and critical habitat.

6. Reach a conclusion about whether species are jeopardized or critical habitat is adversely modified.

7. If necessary, suggest a RPA to the Proposed Action.

2.1.1 Use of Analytical Surrogates

Analytical Surrogates for Salmonids

The effects of the SRBPP RM 71.3 levee repair on salmonids are primarily analyzed using

Standard Assessment Methodology (SAM). The USACE provided the background data, assumptions, analyses, and assessment of habitat compensation requirements for the Federally protected fish species relevant to this consultation.

The SAM was designed to address a number of limitations associated with previous habitat assessment approaches and provide a tool to systematically evaluate the impacts and compensation requirements of bank protection projects based on the needs of listed fish species.

It is a computational modeling and tracking tool that evaluates bank protection alternatives by taking into account several key factors affecting threatened and endangered fish species. By identifying and then quantifying the response of focal species to changing habitat conditions over time, project managers, biologists and design engineers can make changes to project design to avoid, minimize, or provide on- or off-site compensatory mitigation for impacts to habitat parameters that influence the growth and survival of target fish species by life stage and season.

The model is used to assess species responses as a result of changes to habitat conditions, either by direct quantification of bank stabilization design parameters (e.g., bank slope, substrate). The preferred hierarchy of mitigation in all cases is avoid, minimize, compensate onsite and compensate off-site. In the case of most levee projects, most or all of these mitigation strategies are applied due to their large size, challenges associated with completely avoiding and minimizing impacts to species and habitat, temporal delays in habitat function of onsite compensatory mitigation, and limitations associated with being able to provide full compensation at project sites, which warrants the need for some form of off-site compensation.

In 2003, the USACE established a program to carry out “a process to review, improve, and validate analytical tools and models for USACE Civil Works business programs”. Reviews are conducted to ensure that planning models used by the USACE are technically and theoretically sound, computationally accurate, and in compliance with the USACE planning policy. As such, all existing and new planning models developed by the USACE are required to be certified through the appropriate Planning Center of Expertise and Headquarters in accordance with

USACE rules and procedures. The assumptions, model variables, and modeling approaches used in the SAM have been developed to be adapted and validated through knowledge gained from monitoring and experimentation within the SRBPP while retaining the original overall assessment method and framework.

In late 2010, the certification process for the SAM was initiated by the USACE, Sacramento

District in coordination with the Ecosystem Planning Center of Expertise. The process entailed charging a panel of six experts to review the SAM, along with the SAM (version 3.0). The

Review Panel was composed of a plan formulation expert, fisheries biologist, aquatic ecologist, geomorphologist/geologist, population biologist/modeling expert, and software programmer.

A major advantage of the SAM is that it integrates species life history and seasonal flow-related variability in habitat quality and availability to generate species responses to project actions over time. The SAM systematically evaluates the response of each life stage to habitat features affected by bank protection projects.

The SAM quantifies habitat values in terms of a weighted species response index (WRI) that is calculated by combining habitat quality (i.e., fish response indices) with quantity (i.e., bank length or wetted area) for each season, target year, and relevant species/life stage. The fish response indices are derived from hypothesized relationships between key habitat attributes

(described below) and the species and life stage responses. Species 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 (i.e., with or without project), the SAM uses these relationships to determine the response of individual species and life stages to the measured or predicted values of each habitat attribute for each season and target year, and then multiplies these values together to generate an overall species response index.

This index is then multiplied by the linear feet or area of shoreline to which it applies to generate a weighted species response index expressed in feet or square feet. The species WRI provides a common metric that can be used to quantify habitat values over time, compare project conditions to existing conditions, and evaluate the effectiveness of onsite and off-site compensation actions.

The WRI represent an index of a species growth and survival based on a 30-day exposure to post project conditions over the life of the project. As such, negative SAM values can be used as a surrogate to quantify harm to a target fish species by life stage and season. Also, although SAM values represent an index of harm to a species, since the values are expressed as “weighted bankline feet” or “weighted area”, these values can be used to help quantify compensatory conservation actions such as habitat restoration, and are used for that purpose in this BO.

The Effects of the Action section of this BO analyzes the effects of the SRBPP RM 71.3 levee repair project.

Analytical Surrogates for Green Sturgeon

Impacts to the Southern DPS of the North American green sturgeon are also estimated using an analytical surrogate. Although the SAM model does have a green sturgeon component, NMFS has determined that the model may not have the precision to accurately index green sturgeon responses to changes in modeled habitat attributes and that a more rigorous modeling approach needs development. Critical habitat for green sturgeon in the action is designated in the

Sacramento River below ordinary high water (OHW). For this BO, NMFS has determined the amount of critical habitat covered by rock revetment would serve as the best analytical surrogate for impacts to all life stages of green sturgeon. However, the OHW mark could not be collected at the time of this consultation due to the unusually high flows that occurred during the winter of

2017. Therefore, the amount of bare rock revetment will serve as the analytical surrogate for project effects.

2.2 Rangewide Status of the Species and Critical Habitat

This BO examines the status of each species that would be adversely affected by the Proposed

Action. The status is determined by the level of extinction risk that the listed species face, based on parameters considered in documents such as recovery plans, status reviews, and listing decisions. This informs the description of the species’ likelihood of both survival and recovery.

The species status section also helps to inform the description of the species’ current

“reproduction, numbers, or distribution” as described in 50 CFR 402.02. The BO also examines the condition of critical habitat throughout the designated area, evaluates the conservation value of the various watersheds and coastal and marine environments that make up the designated area, and discusses the current function of the essential PBFs that help to form that conservation value.

2.2.1 California Central Valley Spring-run Chinook salmon

Listed as threatened (September 16, 1999, 64 FR 50394), reaffirmed (June 28, 2005, 70 FR

37160).

Designated critical habitat (September 2, 2005, 70 FR 52488)

The Federally listed ESU of Central Valley (CCV) spring-run Chinook salmon and designated critical habitat for this ESU occurs in the Action Area and may be affected by the Proposed

Action. Detailed information regarding ESU listing and critical habitat designation history, designated critical habitat, ESU life history, and VSP (viable salmonid population) parameters can be found in NMFS 2014 Recovery Plan for the Evolutionarily Significant Units of

Sacramento River Winter-Run Chinook salmon, Central Valley Spring-Run Chinook salmon, and the Distinct Population Segment of California Central Valley steelhead.

Historically, spring-run Chinook salmon were the second most abundant salmon run in the

Central Valley and one of the largest on the west coast (CDFG 1990). These fish occupied the upper and middle elevation reaches (1,000 to 6,000 feet) of the San Joaquin, American, Yuba, Feather, Sacramento, McCloud and Pit rivers, with smaller populations in most tributaries with sufficient habitat for over-summering adults (Stone 1872, Rutter 1904, Clark 1929). The Central

Valley drainage as a whole is estimated to have supported spring-run Chinook salmon runs as large as 600,000 fish between the late 1880s and 1940s (CDFG 1998). The San Joaquin River historically supported a large run of spring-run Chinook salmon, suggested to be one of the largest runs of any Chinook salmon on the West Coast with estimates averaging

200,000-500,000 adults returning annually (CDFG 1990).

Monitoring of the Sacramento River mainstem during spring-run Chinook salmon spawning timing indicates some spawning occurs in the river (CDFW, unpublished data, 2014). Genetic introgression has likely occurred here due to lack of physical separation between spring-run and fall-run Chinook salmon populations (CDFG 1998). Sacramento River tributary populations in

Mill, Deer, and Butte creeks are likely the best trend indicators for the CV spring-run Chinook salmon ESU. Generally, these streams have shown a positive escapement trend since 1991, displaying broad fluctuations in adult abundance (CDFW 2016). The Feather River Fish

Hatchery (FRFH) spring-run Chinook salmon population represents an evolutionary legacy of populations that once spawned above Oroville Dam. The FRFH population is included in the

ESU based on its genetic linkage to the natural spawning population, and the potential for development of a conservation strategy (June 28, 2005, 70 FR 37160).

The Central Valley Technical Review Team (TRT) estimated that historically there were 18 or

19 independent populations of CV spring-run Chinook salmon, along with a number of dependent populations, all within four distinct geographic regions, or diversity groups (Lindley et al. 2004). Of these populations, only three independent populations currently exist (Mill, Deer, and Butte creeks tributary to the upper Sacramento River) and they represent only the northern

Sierra Nevada diversity group. Additionally, smaller populations are currently persisting in

Antelope and Big Chico creeks, and the Feather and Yuba rivers in the northern Sierra Nevada diversity group (CDFG 1998). In the San Joaquin River basin, observations in the last decade suggest that spring-running populations may currently occur in the Stanislaus and Tuolumne rivers (Franks 2015).

The CV spring-run Chinook salmon ESU is comprised of two known genetic complexes.

Analysis of natural and hatchery spring-run Chinook salmon stocks in the Central Valley indicates that the northern Sierra Nevada diversity group spring-run Chinook salmon populations in Mill, Deer, and Butte creeks retain genetic integrity as opposed to the genetic integrity of the

Feather River population, which has been somewhat compromised by introgression with the fall-run ESU (Good et al. 2005a, Garza et al. 2007, Cavallo et al. 2011).

Because the populations in Butte, Deer and Mill creeks are the best trend indicators for ESU viability, we can evaluate risk of extinction based VSP in these watersheds. Over the long term, these three remaining populations are considered to be vulnerable to anthropomorphic and naturally occurring catastrophic events. The viability assessment of CV spring-run Chinook salmon conducted during NMFS’ 2010 status review (NMFS 2011a), found that the biological status of the ESU had worsened since the last status review (2005) and recommended that the species status be reassessed in two to three years as opposed to waiting another five years, if the decreasing trend continued. In 2012 and 2013, most tributary populations increased in returning adults, averaging over 13,000. However, 2014 returns were lower again, just over 5,000 fish, indicating the ESU remains highly fluctuating. The most recent status review was conducted in

2015 (NMFS 2016b), which looked at promising increasing populations in 2012-2014; however, the 2015 returning fish were extremely low (1,488), with additional pre-spawn mortality reaching record lows. Since the effects of the 2012-2015 drought have not been fully realized, we anticipate at least several more years of very low returns, which may result in severe rates of decline (NMFS 2016b).

Spring-run Chinook salmon adults are vulnerable to climate change because they over-summer in freshwater streams before spawning in autumn (Thompson et al. 2011). CV spring-run

Chinook salmon spawn primarily in the tributaries to the Sacramento River, and those tributaries without cold water refugia (usually input from springs) will be more susceptible to impacts of climate change. Even in tributaries with cool water springs, in years of extended drought and warming water temperatures, unsuitable conditions may occur. Additionally, juveniles often rear in the natal stream for one to two summers prior to emigrating, and would be susceptible to warming water temperatures. In Butte Creek, fish are limited to low elevation habitat that is currently thermally marginal, as demonstrated by high summer mortality of adults in 2002 and

2003, and will become intolerable within decades if the climate warms as expected. Ceasing water diversion for power production from the summer holding reach in Butte Creek resulted in cooler water temperatures, more adults surviving to spawn, and extended population survival time (Mosser et al. 2013).

Summary of the Central Valley spring-run Chinook salmon ESU viability

In summary, the extinction risk for the CV spring-run Chinook salmon ESU remains at moderate risk of extinction (NMFS 2016b). Based on the severity of the drought and the low escapements as well as increased pre-spawn mortality in Butte, Mill, and Deer creeks in 2015, there is concern that these CV spring-run Chinook salmon strongholds will deteriorate into high extinction risk in the coming years based on the population size or rate of decline criteria (NMFS 2016b).

Critical Habitat and Physical or Biological Features for Central Valley Spring-run Chinook salmon

The critical habitat designation for CV spring-run Chinook salmon lists the PBFs (June 28, 2005, 70 FR 37160), which are described in NMFS 2014 Recovery Plan for the Evolutionarily

Significant Units of Sacramento River Winter-Run Chinook salmon, Central Valley Spring-Run

Chinook salmon, and the Distinct Population Segment of California Central Valley steelhead. In summary, the PBFs include freshwater spawning sites, freshwater rearing sites, freshwater migration corridors, and estuarine habitat. The geographical range of designated critical habitat includes stream reaches of the Feather, Yuba, and American rivers, Big Chico, Butte, Deer, Mill, Battle, Antelope, and Clear creeks, and the Sacramento River, as well as portions of the northern

Delta (June 28, 2005, 70 FR 37160).

Summary of the Value of CV spring-run Chinook salmon Critical Habitat for the Conservation of the Species

Currently, many of the PBFs of CV spring-run Chinook salmon critical habitat are degraded, and provide limited high quality habitat. Features that lessen the quality of migratory corridors for juveniles include unscreened or inadequately screened diversions, altered flows in the Delta, scarcity of complex in-river cover, and the lack of floodplain habitat. Although the current conditions of CV spring-run Chinook salmon critical habitat are significantly degraded, the spawning habitat, migratory corridors, and rearing habitat that remain are considered to have high intrinsic value for the conservation of the species.

2.2.2 California Central Valley Steelhead

Originally listed as threatened (March 19, 1998, 63 FR 13347); reaffirmed as threatened

(January 5, 2006, 71 FR 834).

Designated critical habitat (September 2, 2005, 70 FR 52488).

The Federally listed distinct population segment (DPS) of California Central Valley (CCV) steelhead and designated critical habitat for this DPS occurs in the Action Area and may be affected by the Proposed Action. Detailed information regarding DPS listing and critical habitat designation history, designated critical habitat, DPS life history, and VSP parameters can be found in the NMFS 2014 Recovery Plan for the Evolutionarily Significant Units of Sacramento

River Winter-Run Chinook salmon, Central Valley Spring-Run Chinook salmon, and the

Distinct Population Segment of California Central Valley steelhead.

Historic CCV steelhead run sizes are difficult to estimate given the paucity of data, but may have approached one to two million adults annually (McEwan 2001). By the early 1960s the CCV steelhead run size had declined to about 40,000 adults (McEwan 2001). Current abundance data for CCV steelhead is limited to returns to hatcheries and redd surveys conducted on a few rivers.

The hatchery data is the most reliable because redd surveys for steelhead are often made difficult by high flows and turbid water usually present during the winter-spring spawning period.

CCV steelhead returns to Coleman National Fish Hatchery (NFH) have increased over the last four years, 2011 to 2014. After hitting a low of only 790 fish in 2010, the last two years, 2013 and 2014, have averaged 2,895 fish. Wild adults counted at the hatchery each year represent a small fraction of overall returns, but their numbers have remained relatively steady, typically

200–300 fish each year. Numbers of wild adults returning each year have ranged from 252 to

610 from 2010 to 2014.

Redd counts are conducted in the American River and in Clear Creek (Shasta County). An average of 143 redds have been counted on the American River from 2002–2015 [data from

Hannon et al. (2003), Hannon and Deason (2008), Chase (2010)]. An average of 178 redds have been counted in Clear Creek from 2001 to 2015 following the removal of Saeltzer Dam, which allowed steelhead access to additional spawning habitat. The Clear Creek redd count data ranges from 100-1023 and indicates an upward trend in abundance since 2006 (USFWS 2015).

The returns of CCV steelhead to the Feather River Hatchery experienced a sharp decrease from

2003 to 2010, with only 679, 312, and 86 fish returning in 2008, 2009 and 2010, respectively. In recent years, however, returns have experienced an increase with 830, 1797, and 1505 fish returning in 2012, 2013 and 2014 respectively. Overall, steelhead returns to hatcheries have fluctuated so much from 2001 to 2015 that no clear trend is present.

An estimated 100,000 to 300,000 naturally produced juvenile steelhead are estimated to leave the

Central Valley annually, based on rough calculations from sporadic catches in trawl gear (Good et al. 2005). Nobriga and Cadrett (2001) used the ratio of adipose fin-clipped (hatchery) to unclipped (wild) steelhead smolt catch ratios in the USFWS Chipps Island trawl from 1998 through 2000 to estimate that about 400,000 to 700,000 steelhead smolts are produced naturally each year in the Central Valley. Trawl data indicate that the level of natural production of steelhead has remained very low since the 2011 status review, suggesting a decline in natural production based on consistent hatchery releases. Catches of steelhead at the fish collection facilities in the southern Delta are another source of information on the production of wild steelhead relative to hatchery steelhead (CDFW data: ftp.delta.dfg.ca.gov/salvage). The overall catch of steelhead has declined dramatically since the early 2000s, with an overall average of

2,705 in the last 10 years. The percentage of wild (unclipped) fish in salvage has fluctuated, but has leveled off to an average of 36 percent since a high of 93 percent in 1999.

About 80 percent of the historical spawning and rearing habitat once used by anadromous O.

mykiss in the Central Valley is now upstream of impassible dams (Lindley et al. 2006). Many historical populations of CCV steelhead are entirely above impassable barriers and may persist as resident or adfluvial rainbow trout, although they are presently not considered part of the DPS.

Steelhead are well-distributed throughout the Central Valley below the major rim dams (Good et

al. 2005, NMFS 2016a). Most of the steelhead populations in the Central Valley have a high hatchery component, including Battle Creek (adults intercepted at the Coleman NFH weir), the

American River, Feather River, and Mokelumne River.

California Central Valley steelhead abundance and growth rates continue to decline, largely the result of a significant reduction in the amount and diversity of habitats available to these populations (Lindley et al. 2006). Recent reductions in population size are supported by genetic analysis (Nielsen et al. 2003). Garza and Pearse (2008) analyzed the genetic relationships among

Central Valley steelhead populations and found that unlike the situation in coastal California watersheds, fish below barriers in the Central Valley were often more closely related to below barrier fish from other watersheds than to O. mykiss above barriers in the same watershed. This pattern suggests the ancestral genetic structure is still relatively intact above barriers, but may have been altered below barriers by stock transfers. The genetic diversity of CCV steelhead is also compromised by hatchery origin fish, placing the natural population at a high risk of extinction (Lindley et al. 2007). Steelhead in the Central Valley historically consisted of both summer-run and winter-run migratory forms. Only winter-run (ocean maturing) steelhead currently are found in California Central Valley rivers and streams as summer-run have been extirpated (McEwan and Jackson 1996, Moyle 2002).

Although CCV steelhead will experience similar effects of climate change to Chinook salmon in the Central Valley, as they are also blocked from the vast majority of their historic spawning and rearing habitat, the effects may be even greater in some cases, as juvenile steelhead need to rear in the stream for one to two summers prior to emigrating as smolts. In the Central Valley, summer and fall temperatures below the dams in many streams already exceed the recommended temperatures for optimal growth of juvenile steelhead, which range from 14°C to 19°C (57°F to

66°F). Several studies have found that steelhead require colder water temperatures for spawning and embryo incubation than salmon (McCullough et al. 2001a). In fact, McCullough et al.

(2001) recommended an optimal incubation temperature at or below 11°C to 13°C (52°F to

55°F). Successful smoltification in steelhead may be impaired by temperatures above 12°C

(54°F), as reported in Richter and Kolmes (2005). As stream temperatures warm due to climate change, the growth rates of juvenile steelhead could increase in some systems that are currently relatively cold, but potentially at the expense of decreased survival due to higher metabolic demands and greater presence and activity of predators. Stream temperatures that are currently marginal for spawning and rearing may become too warm to support wild steelhead populations.

Summary of California Central Valley Steelhead DPS viability

All indications are that natural CCV steelhead have continued to decrease in abundance and in the proportion of natural fish over the past 25 years (Good et al. 2005, NMFS 2016a); the long-term trend remains negative. Hatchery production and returns are dominant. Most wild CCV populations are very small and may lack the resiliency to persist for protracted periods if subjected to additional stressors, particularly widespread stressors such as climate change. The genetic diversity of CCV steelhead has likely been impacted by low population sizes and high numbers of hatchery fish relative to wild fish.

In summary, the status of the CCV steelhead DPS appears to have remained unchanged since the

2011 status review, and the DPS is likely to become endangered within the foreseeable future throughout all or a significant portion of its range (NMFS 2016a).

Critical Habitat and Physical or Biological Features for California Central Valley Steelhead

The critical habitat designation for CV spring-run steelhead lists the PBFs (June 28, 2005, 70 FR

37160), which are described in NMFS 2014 Recovery Plan for the Evolutionarily Significant

Units of Sacramento River Winter-Run Chinook salmon, Central Valley Spring-Run Chinook salmon, and the Distinct Population Segment of California Central Valley steelhead. In summary, the PBFs include freshwater spawning sites; freshwater rearing sites; freshwater migration corridors; and estuarine areas.. The geographical extent of designated critical habitat includes: the Sacramento, Feather, and Yuba rivers, and Deer, Mill, Battle and Antelope creeks in the Sacramento River basin; the San Joaquin River, including its tributaries but excluding the mainstem San Joaquin River above the Merced River confluence; and the waterways of the

Delta.

Summary of the Value of California Central Valley Steelhead Critical Habitat for the

Conservation of the species

Many of the PBFs of CCV steelhead critical habitat are currently degraded and provide limited high quality habitat. Passage to historical spawning and juvenile rearing habitat has been largely reduced due to construction of dams throughout the Central Valley. Levee construction has also degraded the value for the conservation of the species of freshwater rearing and migration habitat and estuarine areas as riparian vegetation has been removed, reducing habitat complexity, food resources, and resulting in many other ecological effects. Contaminant loading and poor water quality in Central California waterways poses threats to lotic fish, their habitat and food resources. Additionally, due to reduced access to historical habitats, genetic introgression is occurring because naturally-produced fish are interacting with hatchery-produced fish which has the potential to reduce the long-term fitness and survival of this species.

Although the current conditions of CCV steelhead critical habitat are significantly degraded, the spawning habitat, migratory corridors, and rearing habitat that remain in the Sacramento/San

Joaquin River watersheds and the Delta are considered to have high intrinsic value for the conservation of the species as they are critical to ongoing recovery effort.

2.2.3 Sacramento River Winter-run Chinook Salmon

First listed as threatened (August 4, 1989, 54 FR 32085).

Reclassified as endangered (January 4, 1994, 59 FR 440), reaffirmed as endangered (June 28, 2005, 70 FR 37160).

Designated critical habitat (June 16, 1993, 58 FR 33212).

The Federally listed evolutionary significant unit (ESU) of Sacramento River winter-run

Chinook salmon and designated critical habitat for this ESU occurs in the action area and may be affected by the proposed action. Detailed information regarding ESU listing and critical designation habitat history, designated critical habitat, ESU life history, and viable salmonid population (VSP) parameters can be found in NMFS 2014 Recovery Plan for the Evolutionarily

Significant Units of Sacramento River Winter-Run Chinook salmon, Central Valley Spring-Run

Chinook salmon, and the Distinct Population Segment of California Central Valley steelhead.

Historically, Sacramento River winter-run Chinook salmon (winter-run) population estimates were as high as 120,000 fish in the 1960s, but declined to less than 200 fish by the 1990s (NMFS

2011b) . In recent years, since carcass surveys began in 2001, the highest adult escapement occurred in 2005 and 2006 with 15,839 and 17,296, respectively (CDFG 2012). However, from

2007 to 2013, the population has shown a precipitous decline, averaging 2,486 during this period, with a low of 827 adults in 2011(CDFG 2012). This recent declining trend is likely due to a combination of factors such as poor ocean productivity (Lindley et al. 2009), drought conditions from 2007-2009, and low in-river survival rates (NMFS 2011b). In 2014 and 2015, the population was approximately 3,000 adults, slightly above the 2007–2012 average, but below the high (17,296) for the last 10 years (CDFW 2016).

2014 was the third year of a drought that increased water temperatures in the upper Sacramento

River, and egg-to-fry survival to the RBDD was approximately 5 percent (NMFS 2016c). Due to the anticipated lower than average survival in 2014, hatchery production from LSNFH was tripled (i.e., 612,056 released) to offset the impact of the drought (CVP and SWP Drought

Contingency Plan 2014 ). In 2014, hatchery production represented 83 percent of the total in-river juvenile production. In 2015, egg-to-fry survival was the lowest on record (~4 percent) due to the inability to release cold water from Shasta Dam in the fourth year of a drought. Winter-run returns in 2016 are expected to be low as they show the impact of drought on juveniles from brood year 2013 (NMFS 2016c).

Although impacts from hatchery fish (i.e., reduced fitness, weaker genetics, smaller size, less ability to avoid predators) are often cited as having deleterious impacts on natural in-river populations (Matala et al. 2012), the winter-run conservation program at Livingston Stone

National Fish Hatchery (LSNFH) is strictly controlled by the USFWS to reduce such impacts.

The average annual hatchery production at LSNFH is approximately 176,348 per year

(2001-2010 average) compared to the estimated natural production that passes RBDD, which is

4.7 million per year based on the 2002-2010 average (Poytress and Carrillo 2011). Therefore, hatchery production typically represents approximately 3-4 percent of the total in-river juvenile winter-run production in any given year. However, the average over the last 12 years (about four generations) is 13% with the most recent generation at 20% hatchery influence, making the population at a moderate risk of extinction.

The distribution of winter-run spawning and initial rearing historically was limited to the upper

Sacramento River (upstream of Shasta Dam), McCloud River, Pitt River, and Battle Creek, where springs provided cold water throughout the summer, allowing for spawning, egg incubation, and rearing during the mid-summer period (Yoshiyama et al. 1998). The construction of Shasta Dam in 1943 blocked access to all of these waters except Battle Creek, which currently has its own impediments to upstream migration (i.e., a number of small hydroelectric dams situated upstream of the Coleman Fish Hatchery weir). The Battle Creek Salmon and Steelhead

Restoration Project (BCSSRP) is currently removing these impediments, which should restore spawning and rearing habitat for winter-run Chinook salmon in Battle Creek and possibly establish an additional population in the future. Approximately 299 miles of former tributary spawning habitat above Shasta Dam is inaccessible to winter-run. Yoshiyama et al. (2001) estimated that in 1938, the upper Sacramento River had a “potential spawning capacity” of approximately 14,000 redds equal to 28,000 spawners. Since 2001, the majority of winter-run redds have occurred in the first 10 miles downstream of Keswick Dam. Most components of the winter-run life history (e.g., spawning, incubation, freshwater rearing) have been compromised by the construction of Shasta Dam.

The greatest risk factor for winter-run lies within its spatial structure (NMFS 2011b) . The winter-run ESU is comprised of only one population that spawns below Keswick Dam. The remnant and remaining population cannot access 95 percent of their historical spawning habitat and must therefore be artificially maintained in the Sacramento River by: (1) spawning gravel augmentation, (2) hatchery supplementation, and (3) regulation of the finite cold-water pool behind Shasta Dam to reduce water temperatures.

Winter-run require cold water temperatures in the summer that simulate their upper basin habitat, and they are more likely to be exposed to the impacts of drought in a lower basin environment.

Battle Creek is currently the most feasible opportunity for the ESU to expand its spatial structure but restoration is not scheduled to be completed until 2020. The Central Valley Salmon and

Steelhead Recovery Plan includes criteria for recovering the winter-run Chinook salmon ESU, including re-establishing a population into historical habitats upstream of Shasta Dam (NMFS

2014).

Winter-run Chinook salmon embryonic and larval life stages that are most vulnerable to warmer water temperatures occur during the summer, so this run is particularly at risk from climate warming. The only remaining population of winter-run Chinook salmon relies on the cold water pool in Shasta Reservoir, which buffers the effects of warm temperatures in most years. The exception occurs during drought years, which are predicted to occur more often with climate change (Yates et al. 2008). The shifts in air temperature and precipitation that are anticipated to occur with climate change will likely compromise the quantity and/or quality of winter-run

Chinook salmon habitat available downstream of Keswick Dam. It is imperative for additional populations of winter-run Chinook salmon to be re-established into historical habitat in Battle

Creek and above Shasta Dam for long-term viability of the ESU (NMFS 2014).

Summary of the Sacramento River winter-run Chinook salmon ESU viability

In summary, the extinction risk for the winter-run ESU has increased from moderate risk to high risk of extinction since 2005, and several listing factors have contributed to the recent decline, including drought, poor ocean conditions and hatchery. Large-scale fish passage and habitat restoration actions are necessary for improving the winter-run ESU viability (NMFS 2016c).