Attachment_7-Coleman_NFH_Biological_Opinion_from_NMFS.pdf

Table of Contents

I. BACKGROUND AND CONSULTATION HISTORY

A. Recent history of ESA Consultation of the Proposed Project

II. DESCRIPTION OF THE PROPOSED ACTION

A. Hatchery Facilities

1. Overview

2. Water Supply

3. Water Treatment

4. Water Discharge

5. Broodstock Collection Facilities

6. Adult Holding and Spawning Facilities

7. Incubation and Indoor Rearing Facilities

8. Outdoor Rearing Facilities

9. Fish Transportation Equipment

B. Artificial Propagation Activities

1. Overview

2. Broodstock Collection

3. Fish Sorting

4. Fish Transportation

5. Fish Spawning

6. Carcass Disposal

7. Fish Incubation

8. Fish Rearing

9. Fish Marking

10. Fish Releases

III. ENVIRONMENTAL BASELINE and STATUS of the SPECIES and CRITICAL

HABITAT

A. Action Area B. Endangered Species Act Listing Status and Critical Habitat C. Sacramento River Winter-run Chinook salmon

1. History of Listing Action

2. Life History

3. Range-Wide (ESU) Status and Trends

4. Battle Creek Status and Trends

D. Winter-run Chinook salmon Designated Critical Habitat

1. Access to Spawning Areas in the Upper Sacramento River

2. The Availability of Clean Gravel for Spawning Substrate

3. Adequate River Flows for Successful Spawning, Incubation of Eggs, Fry Development and Emergence, and Downstream Transport of Juveniles

4. Water Temperatures for Successful Spawning, Egg Incubation, and Fry Development

5. Habitat Areas and Adequate Prey that are not Contaminated

6. Riparian Habitat that Provides for Successful Juvenile Development and Survival

7. Unobstructed emigration corridor from Spawning Grounds to the Pacific Ocean

8. Summary of Sacramento River Winter-run Chinook salmon Critical Habitat

E. Central Valley Spring-run Chinook salmon

1. History of Listing Action

2. Life History

3. Range-Wide (ESU) Status and Trends

4. Battle Creek Status and Trends

F. Spring-run Chinook salmon Designated Critical Habitat

1. Spawning Habitat

2. Freshwater Rearing Habitat

3. Freshwater Migration Corridors

4. Estuarine Areas

5. Summary of Central Valley Spring-run Chinook salmon Critical Habitat

G. California Central Valley steelhead

1. History of Listing Action

2. Life History

3. Range-Wide (DPS) Status and Trends

4. Battle Creek Status and Trends

H. California Central Valley steelhead Designated Critical Habitat

1. Spawning Habitat

2. Freshwater Rearing Habitat

3. Freshwater Migration Corridors

4. Estuarine Areas

5. Summary of California Central Valley steelhead Critical Habitat

I. Southern DPS of North American Green Sturgeon

1. History of Listing Action

2. Life History

3. Range-Wide (DPS) Status and Trends

4. Battle Creek Status and Trends

J. Southern DPS of Green Sturgeon Critical Habitat

1. Access to Spawning Areas in the Upper Sacramento River

2. Spawning Substrate

3. Adequate River Flows and Water Quality for Successful Spawning, Incubation of Eggs, and Fry Development

4. Habitat Areas and Adequate Food Resources that are not Contaminated

5. Emigration corridor from Spawning Grounds to the Pacific Ocean

6. Summary of Southern DPS of North American Green Sturgeon Critical Habitat

K. Southern Resident Killer Whales

1. History of Listing Action

2. Life History

3. Range-Wide Status and Trends

L. Factors affecting the Current Status of Listed Species

1. Dams and Habitat Blockage

2. Water Development

3. Anderson-Cottonwood Irrigation District Dam (ACID)

4. Red Bluff Diversion Dam (RBDD)

5. Water Conveyance and Flood Control

6. Land Use Activities

7. Water Quality

8. Hatcheries

9. Ocean Commercial and Sport Harvest

10. Inland Sport Harvest

11. Disease

12. Predation

13. Ocean Productivity

14. Global Climate Change

15. Non-Native Invasive Species

16. Additional Water Quality

17. Summary

M. Factors Affecting the Current Status of the Southern Resident Killer Whale DPS

1. Prey Availability and Quality

2. Sound and Vessel Effects

3. Oil Spills

N. Current Viability of Listed Species

1. Sacramento River Winter-run Chinook salmon ESU

2. Central Valley Spring-run Chinook salmon ESU

3. Current Viability of the California Central Valley steelhead DPS

4. Current Viability of the Southern DPS of North American Green Sturgeon

5. Current Viability and Extinction Risk of the Southern Resident Killer Whale DPS

IV. EFFECTS OF THE ACTION

A. Approach to the Assessment B. Information Available for the Assessment C. Assumptions Underlying This Assessment D. Effects of CNFH Complex Facilities and their Operation on Listed Species

1. Failure of broodstock collection and holding facilities

2. Fish Entrainment

3. Hatchery Water Withdrawals

4. Discharge of Hatchery Effluent

5. Broodstock Congregation and Collection

6. Genetic Effects

7. Disease

8. Competition and Density-Dependent Effects

9. Predation

10. Fisheries

11. Masking

12. Nutrient Cycling

13. Monitoring and Evaluation

14. Beneficial Effects of the CNFH Listed Steelhead Propagation Program………………………………

V. CUMULATIVE EFFECTS

A. Water Diversions B. Agricultural Practices C. Conservation Agreements and Easements D. Aquaculture and Fish Hatcheries E. Increased Urbanization F. Global Climate Change G. Activities within the Nearshore Pacific Ocean

VI. INTEGRATION AND SYNTHESIS

A. Sacramento River Winter-run Chinook salmon ESU

1. Status of Sacramento River Winter-run Chinook salmon ESU

2. Baseline and Cumulative Effects on Winter-run Chinook salmon

3. Summary of Proposed Action Effects on the Winter-run Chinook salmon ESU

4. Assess Risk to the Winter-run Chinook salmon ESU

5. Status of Sacramento River Winter-run Chinook salmon Critical Habitat

6. Project Effects on Sacramento River Winter-run Chinook salmon Critical Habitat

B. Central Valley Spring-run Chinook salmon ESU

1. Status of Central Valley Spring-run Chinook salmon ESU

2. Baseline Stress Regime and Cumulative Effects on the Central Valley Spring-run Chinook salmon ESU Excluding the CNFH Effects As described for Sacramento River winter-run Chinook salmon above, climate change is a key aspect of stress for ESA-listed salmonids in the Central Valley

3. Summary of Proposed Action Effects on the Central Valley Spring-run Chinook salmon ESU

4. Assess Risk to the Central Valley Spring-run Chinook salmon ESU

5. Status of Central Valley Spring-run Chinook salmon Critical Habitat

6. Project Effects on Central Valley Spring-run Chinook salmon Critical Habitat C. California Central Valley steelhead DPS

1. Status of the California Central Valley steelhead DPS

2. Baseline Stress Regime and Cumulative Effects on the California Central Valley steelhead DPS Excluding the CNFH Effects

3. Summary of Proposed Action Effects on the California Central Valley steelhead DPS

4. Assess Risk to the California Central Valley steelhead DPS

5. Status of California Central Valley steelhead Critical Habitat

6. Project Effects on California Central Valley steelhead Critical Habitat

VII. CONCLUSION

VIII. INCIDENTAL TAKE STATEMENT

A. Amount and Extent of Take

B. Take of ESA-listed CNFH-origin California Central Valley steelhead………………………………………192

C. Effect of the Take D. Reasonable and Prudent Measures E. Terms and Conditions

IX. CONSERVATION RECOMMENDATIONS

X. REINITIATION OF CONSULTATION

XI. LITERATURE CITED

List of Figures

Figure 1. Location of the CNFH Figure 2. Physical layout of hatchery facilities at CNFH Figure 4. Schematic of the water delivery system at the CNFH Figure 5. The temporal occurrence of (a) adult and (b) juvenile winter-run in the

Sacramento River Figure 6. The temporal occurrence of adult (a-c) and juvenile (d) Central Valley Spring-run

Chinook salmon in the Sacramento River Figure 7. The temporal occurrence of (a) adult and (b) juvenile California Central Valley steelhead in the Central Valley Figure 8. Estimated California Central Valley steelhead escapement in the upper

Sacramento River based on RBDD counts Figure 9. Returns of natural- and hatchery-origin Oncorhynchus mykiss to Battle Creek for return years 2001-2009 Figure 10. Extinction risk levels corresponding to different amount, duration, and source of hatchery strays Figure 11. Chinook salmon stressors excluding the CNFH related effects (i.e., the figure represents the general baseline stress regime)

List of Tables

Table 1. Annual propagation targets at the Coleman and National Fish Hatchery are presented, including number of adults spawned, initial egg take, and number of juveniles released

Table 2. Winter-run Chinook salmon population estimates and corresponding cohort replacement rates (CRR) for years since 1986

Table 3. Estimated abundance spring-run Chinook salmon in Mill-Deer-Butte creeks, from CDFG Grand Tab (April 2013) with corresponding cohort replacement rates for years since 1986

Table 4. Estimated abundance of “maximum potential” spring-run Chinook salmon and genetically identified spring-run Chinook salmon in Battle Creek, upstream of the CNFH barrier weir, 1995-2009

Table 5. Criteria for assessing the level of risk of extinction for populations of Pacific salmonids

Table 6. Range of extinction and quasi-extinction risk for Southern Resident killer whales in 100 and 300 years, assuming a range in survival rates (depicted by time period), a constant rate of fecundity, between 100 and 400 whales, and a range catastrophic probabilities and magnitudes

Table 7. Estimated take of ESA-listed salmonids resulting from CNFH water diversions from Battle Creek

Table 8. Hatchery risks to winter-run Chinook salmon, affected Viable Salmon Population parameter including Abundance, Diversity, Productivity, and Spatial Structure, indication of whether take is expected, and level of impact to the Evolutionarily Significant Unit

Table 9. Hatchery risks to spring-run Chinook salmon, affected Viable Salmon Population parameter including Abundance, Diversity, Productivity, and Spatial Structure, indication of whether take is expected, and level of impact to the Evolutionarily Significant Unit

Table 10. Hatchery risks to steelhead, affected Viable Salmon Population parameter including Abundance, Diversity, Productivity, and Spatial Structure, indication of whether take is expected, and level of impact to the Distinct Popluation Segment. .183

Table 11. Projected levels and types of incidental take of listed salmonids resulting from artificial propagation programs at Coleman and Livingston Stone National Fish Hatcheries

Table 12. Projected level of annual take of adult CNFH-origin California Central Valley steelhead collected, spawned, and released for the purposes of the CNFH steelhead propagation program, as well as juvenile CNFH-origin California Central Valley steelhead released. ………………………………………………………………….192

I. BACKGROUND AND CONSULTATION HISTORY

This biological opinion constitutes NOAA’s National Marine Fisheries Service (NMFS) consultation with the U.S. Fish and Wildlife (USFWS) regarding the effects of fish propagation programs at the Coleman National Fish Hatchery (CNFH) and effects of collection of natural-origin late fall-run Chinook salmon at Livingston Stone NFH (the CNFH Complex consists of the CNFH and the Livingston Stone NFH) on the federally listed endangered Sacramento River winter-run Chinook salmon (Oncorhynchus tshawytscha) and threatened Central Valley spring-run Chinook salmon (O. tshawytscha) evolutionarily significant units (ESUs) and their designated critical habitats; threatened California Central Valley steelhead (O. mykiss) distinct population segment (DPS) and its designated critical habitat; threatened Southern DPS of North American green sturgeon (Acipenser medirostris) and its critical habitat; and endangered Southern Resident killer whale DPS (Orcinus orca). The hatchery programs are operated to mitigate for impacts resulting from the construction and operation of Shasta and Keswick dams.

USFWS owns and operates the CNFH and Livingston Stone NFH facilities and U.S. Bureau of Reclamation (Reclamation) funds annual maintenance and operations.

This biological opinion has been prepared in accordance with section 7 of the Endangered Species Act (ESA) of 1973 as amended (16 U.S.C. 1531 et seq.) and in compliance with the Data Quality Act (§ 515 of Public Law 106-554). It is based on information provided in a Biological Assessment (BA) and additional information submitted to NMFS by USFWS, on published and unpublished scientific information on listed fishes in the action area, and on other sources representing the best available scientific information. This consultation has incorporated information from several ongoing processes, including the development of NMFS’ Central Valley Salmon and Steelhead Recovery Plan, the Battle Creek Restoration Project, the development of Central Valley-wide monitoring plans for salmon and steelhead, the implementation of a constant fractional marking program in the Central Valley, and the development of Hatchery and Genetic Management Plans (HGMP) in accordance with regulations promulgated under ESA section 4(d) (50 CFR 223.203(b)(5); subsequently referred to as “4(d) rule”). Additional actions which have provided a context for this consultation include the CDFG-NMFS Joint Hatchery Review Committee (2001), NMFS’ hatchery listing policy adopted in 2005 (70 FR 37204; June 28, 2005), the 2005 NMFS status review of Pacific coast salmon and steelhead (Good et al. 2005), the Hatchery Scientific Review Group report (HSRG 2012), and the 2011 NMFS status reviews (NMFS 2011a, 2011b, 2011c). A copy of the administrative record for this consultation is on file with the California Central Valley Area Office.

The 4(d) rule (65 FR 42422, July 10, 2000) does not prohibit the take of ESA-listed fish for a variety of hatchery purposes if a state or Federal agency develops an HGMP and NMFS approves it (September 22, 2000 Southwest and Northwest Region 4(d) Rule Implementation Binder for Threatened Salmon and Steelhead on the West Coast). The USFWS has structured the BA for the CNFH Complex after the format of an HGMP so that it serves the purpose of completing ESA section 7 consultation as well as meeting most of the criteria of limit 5 of the 4(d) rule. Through HGMPs, hatcheries will be managed according to the listed fishes’ status.

This will be determined using the concept of “viable salmonid population” (VSP). Hatchery activities will be scaled to the degree of risk the listed fish face. An HGMP must address the specific criteria outlined in the 4(d) rule. Specifically, an HGMP must: (1) specify the goals and objectives for the hatchery program; (2) specify the donor population’s “critical” and “viable” threshold levels; (3) prioritize broodstock collection programs in a manner that benefits listed fish; (4) specify the protocols that will be used for spawning and raising the fish in the hatchery;

(5) determine the genetic and ecological effects arising from the hatchery program; (6) describe how the hatchery operation relates to fisheries management; (7) ensure that the hatchery facilities can adequately accommodate listed fish if they are collected for the program; (8) monitor and evaluate the HGMP to ensure it accomplishes its objectives; and (9) be consistent with tribal trust obligations. Templates for an HGMP can be found at: http://www.nwr.noaa.gov/Salmon- Harvest-Hatcheries/Hatcheries/HGMP-Template.cfm.

HGMPs for hatchery propagation programs submitted to NMFS under limit 5 of the 4(d) rule may be developed and approved in the following manner. A fish management agency develops an HGMP that meets the 4(d) rule criteria. They send it to NMFS who then requests public review and comment, and determines the National Environmental Policy Act (NEPA) process.

The public input is used to revise the HGMP, if necessary and NMFS writes a letter of approval to the agency that developed the HGMP. The HGMP is then implemented and, as provided in the 4(d) rule, the prohibitions of ESA section 9(a)(1) do not apply to the hatchery program addressed by the HGMP. NMFS then monitors and evaluates the activities covered under the HGMP. Hatchery propagation programs for species listed as endangered, such as CNFH Complex’s winter-run Chinook salmon program, go through a similar process, but are covered under ESA section 10(a)(1)(A) through issuance of a research and enhancement permit, as opposed to coverage under the 4(d) rule. The USFWS and NMFS have determined the HGMP for winter-run Chinook salmon will be completed with the addition of the information in the 2013 renewal of the ESA section 10 permit, and associated ESA section 7 biological opinion for the renewal of the permit. The ESA section 10 permit and associated ESA section 7 biological opinion will cover take of winter-run Chinook salmon for the purpose of propagation at Livingston Stone NFH as well as incidental take of other listed species as a result of that hatchery propagation program. Therefore, these activities are not part of the proposed action for this biological opinion. CNFH is not currently including listed natural-origin fish in the steelhead program, however, the CNFH produced steelhead are also considered part of the federally listed DPS, although there is not currently a take prohibition for adipose-fin clipped hatchery steelhead; therefore, an HGMP for adipose fin clipped hatchery steelhead does not need to be authorized under the 4(d) rule. However, NMFS agrees with the recent HSRG report (2012) recommendation that all Federal/State hatchery programs submit an HGMP. For the CNFH Complex, this biological opinion will serve as part of the review process for HGMPs for the propagation of fall-run and late fall-run Chinook salmon and adipose-fin clipped hatchery steelhead in addition to any review that the USFWS must complete under NEPA, including public review and comment.

The USFWS has determined that the proposed action is likely to affect federally listed salmon, steelhead, and their designated critical habitats; that federally listed green sturgeon and its critical habitat may also be affected; and that federally listed killer whales may also be affected.

Therefore, this biological opinion will address these federally listed species and designated critical habitat. USFWS determined that the proposed action will have no effect to critical habitat designated for killer whales. Based on this determination, and since critical habitat designated for federally listed killer whales is outside the action area, this biological opinion will http://www.nwr.noaa.gov/Salmon-Harvest-Hatcheries/Hatcheries/HGMP-Template.cfm http://www.nwr.noaa.gov/Salmon-Harvest-Hatcheries/Hatcheries/HGMP-Template.cfm not include any further discussion of critical habitat for killer whales. The likelihood and magnitude of impacts from the fish propagation programs that are part of the proposed action depend on overlap of project activities with each species’ spatial and temporal distributions, habitat and resource needs, and life-history requirements. The framework used by NMFS to assess impacts from fish propagation programs focuses on those areas of significant resource and life-history commonality, as these are the areas where impacts are most likely and foreseeable.

Impacts to federally listed Sacramento River winter-run Chinook salmon, Central Valley spring-run Chinook salmon and California Central Valley steelhead were evaluated for the following ten general areas of risk: (1) Hatchery Facilities and Facility Operations (which includes hatchery failure, fish entrainment, hatchery water withdrawals, and discharge of hatchery effluent); (2) Broodstock Collection; (3) Genetic Introgression; (4) Disease; (5) Competition/Density-Dependent Effects (including ocean competition); (6) Predation; (7) Fisheries; (8) Masking; (9) Nutrient Cycling; and (10) Monitoring and Evaluation. Risk assessment of impacts of propagation programs conducted at the CNFH to North American green sturgeon was initially considered in all areas of potential impact, but was subsequently focused to possible effects of predation by hatchery fish upon juvenile green sturgeon, as this is the area of potential impact based on life-history overlap. Impacts to Southern Resident killer whales is probable only in the area of prey availability, with fishes produced at the CNFH likely contributing a beneficial effect to prey availability. Detrimental impacts could occur in the event of a broodstock production failure.

A. Recent history of ESA Consultation of the Proposed Project

On August 28, 2000, USFWS requested an extension of the 1999 CNFH biological opinion (NMFS 1999c), which covered the California Central Valley steelhead, and fall-run and late fall-run Chinook salmon programs, in order to complete work on the BA (and to include effects to the newly listed threatened spring-run Chinook salmon (September 1999), which also was to serve as a template for HGMPs for programs at both CNFH and Livingston Stone NFH.

On December 19, 2000, NMFS received a summary from USFWS, dated December 14, 2000, of comments, modifications and revisions resulting from the agency review process of the BA.

These modifications were incorporated into the BA draft prior to public distribution. USFWS extended the public review comment period on the BA to January 29, 2001.

On December 27, 2000, NMFS extended coverage of the 1999 CNFH biological opinion through March 31, 2001. No additional impacts to listed fish or critical habitat over those previously addressed were expected to occur as a result of this extension.

On March 12, 2001, USFWS requested an extension of the 1999 CNFH biological opinion, in order to incorporate public comments into the BA. On March 19, 2001, NMFS granted the extension of the biological opinion through September 12, 2001.

On June 13, 2001, NMFS received the BA for the CNFH and Livingston Stone NFH artificial propagation and captive broodstock programs (which added the endangered winter-run Chinook salmon program at Livingston Stone NFH), including the request from USFWS to review a draft biological opinion prior to finalizing the document. On June 27, 2001, NMFS received a copy of key appendices to the BA from USFWS, for insertion to the final document. The BA was developed following the format of a HGMP template.

On October 22, 2001, NMFS extended the ESA coverage of the 1999 CNFHCNFH biological opinion through December 31, 2001. The biological opinion was further extended through March 1, 2002, in order to allow NMFS time to complete their analysis of the effects of the proposed hatchery actions on listed salmonids.

On December 20, 2001, NMFS received an addendum to the June 2001 BA, dated December 5, 2001, from USFWS explaining its intent to allow passage of adult hatchery steelhead above the CNFHCNFH barrier weir in Battle Creek as a population supplementation action to be incorporated into the Battle Creek Fishery Management Plan.

On December 21, 2001, NMFS received a description from USFWS of the proposed collection and tissue sampling protocol for non-marked steelhead at CNFHCNFH, for purposes of genetic monitoring using microsatellite deoxyribonucleic acid (DNA) techniques, and for comparison with CNFHCNFH steelhead to determine the potential for using the hatchery stock in restoration efforts in Battle Creek.

In letters to USFWS dated January 23, 2002, and February 5, 2002, NMFS clarified the Federal non-listed status of CNFHCNFH steelhead, and the need for a scientific basis regarding further hatchery steelhead supplementation in Battle Creek.

On February 7, 2002, NMFS received a letter from USFWS dated January 24, 2002, informing NMFS of the commitment by USFWS to re-initiate formal consultation for operation of CNFHCNFH and Livingston Stone NFH upon completion of the Battle Creek Salmon and Steelhead Restoration Project. This action was prompted by concerns of the Battle Creek Working Group (BCWG) regarding the timing of future ESA section 7 consultations for CNFH compared with restoration actions in Battle Creek.

On April 15, 2002, USFWS requested NMFS’ participation in a multi-agency meeting to investigate and recommend a strategy for managing returning steelhead adults in excess of broodstock needs at CNFH, for the 2002-2003 spawning season. A letter of confirmation for the meeting, dated May 9, 2002, was received by NMFS on May 13, 2002.

On May 15, 2002, representatives from USFWS, Reclamation, California Department of Fish and Game (CDFG), and NMFS met to discuss potential strategies for managing excess adult CNFH steelhead during the 2002-2003 spawning season. Eleven management alternatives were suggested, and a decision tree was developed to further discuss the alternatives at a planned future meeting.

On June 11, 2002, NMFS extended ESA incidental take coverage of the 1999 biological opinion through September 1, 2002, in order to analyze the effects of incorporating natural steelhead as hatchery broodstock on the continued existence of threatened and endangered salmonid species in the upper Sacramento River basin.

On July 11, 2002, representatives from USFWS, Reclamation, CDFG, and NMFS met to discuss potential options related to passing adult hatchery steelhead above the CNFH barrier weir.

Discussion focused on current natural steelhead abundance, the carrying capacity of Battle Creek, the broodstock history of CNFH steelhead, current genetic information, and development of a study plan regarding the passing of hatchery steelhead into upper Battle Creek.

On August 16, 2002, NMFS received a draft monitoring and evaluation plan from USFWS for CNFH steelhead in excess of hatchery broodstock needs. On September 4, 2002, USFWS submitted a letter of justification to NMFS on the proposal to allow passage of surplus hatchery steelhead above the CNFH barrier weir, based on the origin and genetic relationship of the hatchery steelhead to the natural steelhead population in Battle Creek.

On September 24, 2002, a consensus decision was reached among USFWS, Reclamation, CDFG, and NMFS to release adult hatchery steelhead above the CNFH during the 2002-2003 migration and spawning season, and on October 31, 2002, NMFS co-signed a letter of support for this action with USFWS, Reclamation, and CDFG.

In a letter to NMFS dated July 30, 2003, USFWS initiated Essential Fish Habitat (EFH) consultation on the facilities and operations of the CNFH and Livingston Stone NFH.

On September 11, 2003, representatives of USFWS, CDFG, the NMFS Protected Resources Division, and the NMFS Southwest Fisheries Science Center (SWFSC) attended a Battle Creek steelhead genetics and CNFH operations meeting. A presentation was given on the 2002-2003 Battle Creek steelhead genetic tissue analysis results, and discussion was held on a draft steelhead monitoring and evaluation plan and proposed amendment to hold natural steelhead broodstock at CNFH prior to spawning.

On October 1, 2003, NMFS received a modification to the 2001 BA from USFWS for the collection of natural steelhead by CNFH for incorporation as broodstock for the hatchery steelhead program.

On October 8, 2003, NMFS gave a presentation to the California Bay-Delta Authority (CALFED) at the Battle Creek Workshop on the issues expected to be addressed in the CNFH and Livingston Stone NFH biological opinion at the Battle Creek Workshop.

On December 16, 2004, NMFS received a letter from USFWS, dated December 13, 2004, on a modification to the broodstock collection strategy for natural origin late fall-run Chinook salmon (O. tshawytscha) at CNFH.

On January 6, 2004, NMFS approved a December 23, 2003, request from USFWS, for authorization of tissue collection from incidentally trapped steelhead at Keswick Dam, for the purpose of genetic analysis of upper mainstem Sacramento River, Battle Creek and CNFH steelhead.

In a letter dated January 28, 2005, USFWS informed NMFS of a modification to their fish salvage plan for CNFH through an experimental “real-time” fish rescue effort that was conducted in May, June, and August of 2005.

In a letter dated June 20, 2005, USFWS informed NMFS of the results of planting CNFH steelhead into Keswick Reservoir. Based upon steelhead escapement from the reservoir and their recapture downstream, USFWS discontinued the outplanting effort to prevent impact to the natural anadromous steelhead in the upper Sacramento River.

In a letter to NMFS, dated April 7, 2006, USFWS provided a revised estimate of incidental take of ESA-listed anadromous salmonids at the CNFH water intakes, precipitated by a forced change in hatchery operations. Damage to the Pacific Gas & Electric Company’s (PG&E) Coleman Powerhouse on December 2, 2005, prevented routing of stream flow through the powerhouse and made the hatchery’s primary water supply intake (Intake 1) non-functional. CNFH relied on its unscreened backup water supply, Intake 2, until the repairs were completed and Intake 1 was made functional again.

In a letter to NMFS, dated December 1, 2008, USFWS informed NMFS of a modification to the CNFH late fall-run Chinook salmon release strategy, by the timing of releases with high flow events and peak late fall-run smoltification. USFWS would initiate a study concurrent with implementation of the modified release strategy to evaluate effects to natural-origin salmonids in the Sacramento River.

In a letter sent to NMFS in February 2009, USFWS provided notice of a temporary change to the strategy of releasing general production fall-run Chinook salmon (O. tshawytscha). USFWS intended to transport a portion (approximately 1.5 million fish, 10.7 percent of total production) of the hatchery’s general production fall-run Chinook salmon to the San Pablo Bay, where they would be acclimated for a short period of time and then released. An attachment to the letter provided an analysis of effects to ESA-listed salmonids.

In a letter dated March 25, 2010, USFWS informed NMFS of the use of an unscreened water intake at the CNFH for the period February 8, 2010, through March 31, 2010. Attached to that letter were estimates of entrainment of ESA-listed salmonids and a description of planned efforts to salvage entrained fishes.

In a letter dated July 12, 2010, USFWS informed NMFS of the planned use of an unscreened hatchery intake from July 22, 2010, to September 22, 2010. Use of the unscreened, back up intake would be necessitated by the scheduled maintenance of the PG&E powerhouse, which would dewater the hatchery’s primary intake. Attached to the letter were estimates of entrainment of listed salmonids in Battle Creek. Based on the low numbers of fishes emigrating from Battle Creek at that time of year and the relatively high amount of effort required to conduct an effective salvage operation, USFWS proposed to not implement a salvage effort.

On July 15, 2010, USFWS sent NMFS a report of fish salvage at the CNFH canal associated with the operation of an unscreened hatchery water intake for the period February 8, 2010, through March 31, 2010.

In a letter dated December 22, 2010, USFWS requested from NMFS a one-year variance to the production limit for steelhead to be released from the CNFH in 2011. The estimated production of brood year 2010 steelhead was approximately 27,000 over the upper production limit, as defined in the 1999 biological opinion for the CNFH artificial production programs. Included with the request was a risk analysis, which concluded that there would be negligible risks to listed salmon and steelhead in the upper Sacramento River.

On July 27, 2011, USFWS submitted an updated Biological Assessment for the CNFH Complex, and requested formal consultation.

From April 2012 through August, 2013, periodic discussions were held between UFWS and NMFS to clarify elements of the proposed action, effects analysis, scope of incidental take and other elements related to the incidental take statement.

II. DESCRIPTION OF THE PROPOSED ACTION

The CNFH Complex consists of the CNFH and the Livingston Stone NFH. The CNFH, authorized by the Central Valley Project (CVP), was constructed by Reclamation to partially mitigate for the loss of 187 miles of salmonid spawning and rearing habitat that was blocked after the construction of Shasta Dam (Skinner 1958; USFWS 2001b). The hatchery was constructed in 1942 on Battle Creek, near the city of Anderson, Shasta County, 5.8 river miles (RM) from the confluence with the Sacramento River (Figure 1), and fish culture operations began in 1943. During its history, CNFH has implemented propagation programs for winter-, spring-, fall- and late fall-run Chinook salmon and steelhead. Currently, CNFH manages two integrated-harvest programs: the non-listed fall-run Chinook salmon and late fall-run Chinook salmon programs, and one segregated program: the listed steelhead program. USFWS produces fall- and late fall-run Chinook salmon primarily to contribute to harvest in the ocean commercial fishery, the ocean sport fishery, and the freshwater sport fishery. Steelhead are produced primarily for harvest in the freshwater sport fishery. In addition, fish may also be reared for the purpose of research. CNFH is operated by USFWS.

The Livingston Stone NFH was constructed in 1997 at the base of Shasta Dam to assist recovery efforts for endangered winter‐run Chinook salmon. Assuring that hatchery origin winter-run Chinook salmon would return to the upper Sacramento River to supplement the natural population resulted in the need to relocate the program from CNFH on Battle Creek to a location directly on the Sacramento River. Thus, Livingston Stone NFH was constructed in 1997.

Reclamation is responsible for the funding of operations related to salmon and steelhead propagation at the CNFH and the Livingston Stone NFH. As described in the Background and Consultation History section of this biological opinion, renewal of the ESA section 10 permit and associated ESA section 7 biological opinion will cover take of winter-run Chinook salmon for the purpose of propagation at the Livingston Stone NFH as well as incidental take of listed species as a result of that hatchery propagation program. Therefore, these activities are not part of the proposed action for this biological opinion. For the Livingston Stone NFH, the following discussion of hatchery facilities and operations focuses on collection of natural-origin late fall-run Chinook salmon that may occur at the Keswick Dam fish trap located on the Sacramento River.

A. Hatchery Facilities

1. Overview

a. CNFH

CNFH facilities include the main hatchery building containing incubation stacks and trays and fiberglass tanks for early-rearing; the administration building; the feed storage building; the garage, warehouse and storage buildings; the spawning building; the maintenance shop; the electrical sub-station and generator buildings; the ozone water treatment plant and associated structures; and three staff residences. Other structures for fish propagation include: twenty-eight 15-feet (ft) by 150-ft concrete raceways; thirty 8-ft by 80-ft concrete raceways; a pollution abatement pond, and facilities for congregating, collecting, holding, and spawning broodstock (Figure 2). Additionally, the USFWS California-Nevada Fish Health Center uses four buildings located on the hatchery property, including two used for office/laboratories and one wet lab.

There is also on-station housing for hatchery staff.

2. Water Supply

a. CNFH

CNFH has water rights to withdraw up to 122 cubic feet per second (cfs) from Battle Creek, including 13 cfs that is diverted through the hatchery intake and delivered to downstream water users. Three intake structures and associated conveyance facilities are used to divert and convey water directly from the Coleman Powerhouse tailrace and Battle Creek (Figure 4). USFWS monitors water use at the hatchery to ensure compliance with the water rights.

The CNFH primary intake (Intake 1) is located in the tailrace of the PG&E Coleman Powerhouse, which empties into Battle Creek approximately 1.6 miles upstream of the hatchery property. Intake 1 is unscreened, however, it is inaccessible to anadromous salmonids from the downstream direction by a juvenile fish barrier and an adult salmonid exclusion weir, which prevent listed salmonids from accessing an area where they could become entrained. CNFH Intake 2 (unscreened) is located on the south bank of Battle Creek, in close proximity to Intake 1.

Intake 2 draws water directly from Battle Creek, and is used as an emergency back-up to Intake

1. The design of Intake 2 prevents diversion of water simultaneous with Intake 1. Intake 2 supplies water to the hatchery only during periods when water cannot be supplied through Intake 1 (e.g., emergency (failure of canal) or powerhouse maintenance). Intake 3 is screened and draws water directly from Battle Creek, approximately 0.4 miles downstream of Intake 2, and 1.2 miles upstream of the hatchery.

Water from all three intakes can be shunted to the ozone water treatment facility or sent directly to various fish-rearing areas at CNFH. The water delivery system at CNFH has numerous piping interconnections between facilities. These interconnections allow water to be diverted from the canal to the sand traps, to bypass the water treatment system, and to be reused from the 15-ft by 150-ft raceways to the 8-ft by 80-ft raceways.

The water delivery system and water treatment plant at CNFH are equipped with numerous alarms to alert hatchery staff in the event of power outages or low water supply.

Figure 1. Location of the CNFH.

Figure 2. Physical layout of hatchery facilities at CNFH.

Figure 3. Schematic of the water delivery system at the CNFH.

Pollution Abatement Pond

CA-NV Fish Health Center

Cold Storage/Freezer Building

Equipment Storage Building

Residences

Hatchery Building

15’ x 150’ Raceways (28)

8’ x 80’ Raceways

(30)

Shop

Administration Building

Kiosk

Adult Holding Ponds

Pre-release Pond

Spawning Building

Equipment Storage Building

Ozone Water Treatment Building

Sand Filter

Electrical Sub-station

Barrier Weir Battle Creek

New Fish Ladders

N

In 2009, USFWS completed modifications to the CNFH intakes and water conveyance systems to improve protection for natural-origin fish in Battle Creek and improve efficiency, reliability, and flexibility of water deliveries for hatchery operations. The diversion capacity of Intake 1 was increased from 50 to 122 cfs, and a new 400-ft pipeline was extended downstream to discharge into the pipeline from Intake 3. The increased capacity of Intake 1 enables, under normal operations, the full allotment of water to the CNFH to be diverted from the tailrace of the PG&E powerhouse (i.e., water that has already been diverted through the PG&E hydroelectric project system), thereby reducing the need for additional diversions directly from Battle Creek.

Intake 3 was rebuilt with a new fish screen that meets the screening criteria of NMFS and CDFG.

The screening of Intake 2, a secondary back-up to intakes 1 and 3, will be completed as a second phase of the project, contingent on funding. The intake and water delivery modifications completed in 2009 afford improved protections for naturally produced fish in Battle Creek and provide a reliable supply of high-quality water to satisfy operational needs at CNFH.

USFWS has developed a salvage plan for rescuing fish from the water delivery canal and sand traps following the recommendations in the 1999 CNFH Biological Opinion (NMFS 1999c).

Fish rescues are carried out by CNFH staff or the Red Bluff Fish and Wildlife Office (RBFWO), who notify NMFS when there is a powerhouse emergency or planned maintenance action that would necessitate the use of unscreened Intake 2. Annual maintenance of the PG&E powerhouse is coordinated with CNFH, and generally occurs during two weeks of low flow when few anadromous fishes are emigrating from Battle Creek into the Sacramento River.

Fish salvage of the delivery canal takes place when water demand can be supplied fully by Intake 3 and fish rescue in the settling basins must be conducted when Intake 3 is not in use. The canal and traps require some draining and dewatering, and fish rescue is often complicated by sediment and submerged vegetation. Rescue techniques may include the use of dip nets, fyke nets, beach seines, and electroshocking.

3. Water Treatment

a. CNFH

The water supply at CNFH is treated with a combination of settling, filtration, and ozonation to remove silt, sediment and pathogens that impact fish reproduction and health. To reduce sediment in the hatchery water supply and to alleviate recurrent disease problems, CNFH uses a water treatment facility capable of filtering 45,000 gpm and ozonating 30,000 gpm. Ozone treatment kills viral, bacterial, and protozoan organisms that could infect fish being reared in the hatchery. Operation of the ozone water treatment facility has substantially reduced the occurrence of disease in hatchery production and the potential for disease transmission to naturally-produced stocks. Since 1999, the year that near-production capacity of the new ozone facility was first achieved, juvenile salmonids propagated at CNFH have been reared and released with no incidence of disease.

4. Water Discharge

a. CNFH

CNFH follows a Monitoring and Reporting Program and operates under a Best Management Practices (BMPs) Plan to meet its waste discharge management requirements under a National Pollution Discharge Elimination System permit (NPDES No. CAG135001) issued by the California Regional Water Quality Control Board (CRWQCB). CNFH directs 3.3 million gallons per day (mgd) of its daily 40.8 mgd flow-through effluent into its pollution abatement pond for filtering out large particulate matter associated with raceway cleaning. Water that is not diverted to the pollution abatement pond is discharged directly into Battle Creek through an overflow channel, the fish ladder, and a separate wastewater ditch. Effluent released from the hatchery must meet requirements for water temperature, pH (the measure of the acidity or basicity of an aqueous solution), suspended solids, and chemical oxygen demand (CDO) in the receiving stream’s mixing zone (USFWS 2001b). CNFH has also developed and follows a Spill Prevention Control and Countermeasure Plan.

5. Broodstock Collection Facilities

a. CNFH

The facilities for congregating and collecting broodstock at the CNFH consist of a barrier weir, fish ladder, and holding ponds. The CNFH barrier weir and fish ladder are located approximately six miles up from Battle Creek’s confluence with the Sacramento River. The weir is permanent and extends across the full width of Battle Creek (approximately 90 ft). The primary purpose of the barrier weir is to congregate salmonids and divert them into the hatchery’s adult collection and holding ponds. USFWS, working cooperatively with Reclamation, completed modifications to the CNFH barrier weir and fish ladder in September 2008. The modification to the barrier weir is intended to improve the capability of controlling fish migration in Battle Creek. Modifications included the addition of a 2-foot-wide, lipped cap to the crest of the barrier weir and an overshot gate, which is used to regulate attraction flows at the entrance of the fish ladder. A new bifurcated fish ladder was also constructed; one fork leads directly to the existing CNFH adult holding ponds and the other provides access to Battle Creek upstream of the barrier weir. Additional modifications were included to enable lamprey (Lampetra spp.) to migrate through the fish ladder. A monitoring vault and viewing window is also included to support monitoring of fish passing above the hatchery. The reconstructed barrier weir was designed to block the passage of upstream migrating salmonids at flows up to 800 cfs and the new fish ladder was designed to efficiently attract and pass fish upstream, using criteria equivalent to that of upstream fish ladders associated with the Battle Creek Salmon and Steelhead Restoration Project.

b. Livingston Stone NFH

In addition to broodstock collection in Battle Creek, natural-origin late fall-run Chinook salmon may be collected at the Keswick Dam fish trap located on the Sacramento River and transported for propagation at the CNFH. The Keswick Dam fish trap and associated structures are located in the center of the dam between the powerhouse and the spillway. Broodstock collection facilities consist of a twelve-step fish ladder, a brail-lift, and a 1,000-gallon fish-tank elevator.

6. Adult Holding and Spawning Facilities

Adult holding and spawning facilities at CNFH consist of five holding ponds of various configurations and a fully-mechanized facility for crowding, sedating, sorting, and spawning collected adults. Upon ascending the hatchery’s adult collection ladder and lower part of Pond 2, salmonids ultimately enter Pond 3, which measures 200-ft by 36-ft (a volume of 30,600 cubic-ft [ft3]). Fishes collected in Pond 3 are routed into the spawning building using mechanized crowders. The spawning building includes a spawning and sorting facility. A hydraulic lift located in the spawning building raises fish into a sedation tank infused with carbon dioxide (CO2). Non-target fish can be returned immediately to Battle Creek during the initial sorting process by diverting them down a tube emptying into Battle Creek above the CNFH barrier weir.

Hatchery broodstock can either be spawned immediately (e.g., if fully mature) or shunted to Pond 3, Pond 4 or Pond 5 until they’re ready for spawning. Ponds 4 and 5 measure 81.5-ft by 41-ft each (23,390 ft3) and are also enclosed in the spawning building. Pond 1, also called the pre-release pond, measures 201-ft by 60-ft, and is used to hold post spawn steelhead during the recondition of those fish. Pond 1 has concrete sides and a gravel bottom.

7. Incubation and Indoor Rearing Facilities

a. CNFH

Egg incubation facilities are located in the hatchery building. Incubation units consist of 178 sixteen-tray vertical fiberglass incubators (Heath Incubation Trays). The top tray of each incubation stack is not used to limit the exposure of incubating eggs to light and silt. Also located in the hatchery building are sixty-seven 16-ft by 3.33-ft fiberglass tanks used for early-rearing of steelhead.

8. Outdoor Rearing Facilities

a. CNFH

Outdoor rearing units include twenty-eight 15-ft by 150-ft raceways and thirty 8-ft by 80-ft outdoor raceways. The raceways are constructed of concrete, surrounded by fencing, and covered with a network of wire to reduce terrestrial and avian predation. The 15-ft by 150-ft raceways are approximately 4 ft deep at the upstream end and 4 ft 9 inches deep at the downstream end, containing approximately 5,600 ft3. The 8-ft by 80-ft raceways hold approximately 1,148 ft3 of water.

9. Fish Transportation Equipment

CNFH has two trucks that are used to transport fish; a 2002 Freightliner (tank capacity of 2,000 gallons) and a 1998 Freightliner (tank capacity of 1,500 gallons). Distribution trucks are used for transporting steelhead trout to the Sacramento River at Bend Bridge (RM 258) and for transporting a portion (approximately 10 percent) of the fall-run Chinook salmon to the San Pablo Bay for release. Occasionally, fall and late fall-run Chinook salmon are transported to alternative off-site release locations as part of various research projects. These trucks are also used to transport natural-origin late fall-run Chinook salmon from the Keswick Dam fish trap to

CNFH.

B. Artificial Propagation Activities

1. Overview

a. CNFH

The fall- and late fall-run Chinook salmon and steelhead propagation programs at the CNFH are intended to partially mitigate for the impacts of Shasta Dam on anadromous Chinook salmon and steelhead. Fall- and late fall-run Chinook salmon propagation programs are integrated-harvest type programs. The goal of the fall and late fall-run Chinook salmon programs is to contribute to harvest in the Sacramento River sport fishery and sport and commercial ocean fisheries. The steelhead propagation program at the CNFH is currently operated as a segregated-harvest type program. The CNFH steelhead program is intended to contribute to sport fisheries in the Sacramento River and Sacramento-San Joaquin Delta (Delta). The annual production goals are 12 million Central Valley fall-run Chinook salmon smolts, 1 million Central Valley late fall-run Chinook salmon smolts, and 600,000 steelhead smolts (Table 1).

Table 1. Annual propagation targets at the Coleman and National Fish Hatchery are presented, including number of adults spawned, initial egg take, and number of juveniles released. Also shown are target release timing, life stage and size, and release location.

Release # of Adults

(1 ♀ : 1 ♂) Production

Target1 Month Size Location

Fall-run Chinook salmon

5,200 12,000,000 April 75 mm.

90 / lb 88 mm.

60 / lb.

90 percent - Battle Creek

10 percent - San Pablo Bay

Late fall-run Chinook salmon

540 1,000,000 December 135 mm.

13 / lb

Battle Creek

Steelhead

400-800a

600,000

January

200 mm.

4 / lb

Sacramento River at Bend (RM 258) a the range of 400 to 800 fish is the minimum number required for meeting the production objectives

2. Broodstock Collection

1 Actual production may differ from release targets by +/- 15 percent, due to variations in fecundity and survival (Service 2001b).

The Coleman barrier weir and its associated fish ladders are located approximately 5.8 miles upstream from the confluence of Battle Creek and the Sacramento River. The weir is permanent, and extends across the full width of Battle Creek (approximately 90 ft). The barrier weir obstructs passage of adult salmonids to the ladder leading to upper Battle Creek (upstream of the hatchery) during broodstock collection and diverts them to a fish ladder leading to the hatchery’s adult holding ponds. This method of broodstock collection is believed to provide a representative (unbiased) sample of all adults attempting to ascend Battle Creek past the CNFH.

Upstream passage is blocked at the CNFH barrier weir from August 1 through February 28.

From March through July, fish are allowed to ascend Battle Creek past the barrier weir using a fish ladder. To obtain a representative sample of each broodstock, fall- and late fall-run Chinook salmon are collected at CNFH throughout the duration of arrivals at the hatchery.