APPENDIX B1-Permits Station Humboldt Bay Maintenance Dredging.pdf

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April 6, 2023 Refer to NMFS No: WCRO-2023-00135

Captain Daniel R. Ursino Captain United States Coast Guard 1301 Clay Street, Suite 700N Oakland, California 94612-5203

Re: Endangered Species Act Section 7(a)(2) Biological Opinion, and Magnuson-Stevens

Fishery Conservation and Management Act Essential Fish Habitat Response for the United States Coast Guard Station Humboldt Bay Maintenance Dredging Project (2023-2032) in Humboldt County, California

Dear Captain Ursino:

Thank you for your letter of January 26, 2023, requesting formal consultation with NOAA’s National Marine Fisheries Service (NMFS) pursuant to section 7 of the Endangered Species Act of 1973 (ESA) (16 U.S.C. 1531 et seq.) for the United States Coast Guard Station (USCG) Humboldt Bay Maintenance Dredging (2023-2032) Project. Thank you, also, for your request for consultation pursuant to the essential fish habitat (EFH) provisions in Section 305(b) of the Magnuson-Stevens Fishery Conservation and Management Act (MSA)(16 U.S.C. 1855(b)) for this action. This letter transmits NMFS’ final biological opinion and EFH response for the proposed USCG Station Humboldt Bay Maintenance Dredging (2023-2032) Project (Project).

The enclosed biological opinion describes NMFS’ analysis of effects on threatened Southern Oregon/Northern California Coast (SONCC) coho salmon (Oncorhynchus kisutch), California Coastal (CC) Chinook salmon (O. tshawytscha), Northern California (NC) steelhead (O.mykiss), Southern Distinct Population Segment (SDPS) of North American green sturgeon (Acipenser mediostris) and their designated critical habitat in accordance with section 7 of the ESA. Based on the best scientific and commercial information available, NMFS concludes that the proposed action is not likely to jeopardize the continued existence of SONCC coho salmon, CC Chinook salmon, NC steelhead, SDPS green sturgeon, nor is the project likely to destroy or adversely modify designated critical habitat for these species. NMFS expects the proposed action would result in incidental take of SONCC coho salmon, CC Chinook salmon, NC steelhead, and SDPS green sturgeon. An incidental take statement with terms and conditions is included with the enclosed biological opinion.

The enclosed EFH consultation was prepared pursuant to section 305(b) of the MSA. The proposed action includes areas identified as EFH for species managed under the Pacific Coast Salmon Fishery Management Plan (FMP), Pacific Coast Groundfish FMP, and Coastal Pelagic Species FMP. Based on our analysis, NMFS concludes that the project would adversely affect EFH of all three FMPs and has provided two EFH Conservation Recommendations.

Please contact Matt Goldsworthy, Northern California Office, Arcata, via email at Matt.Goldsworthy@noaa.gov if you have any questions concerning this consultation, or if you require additional information.

Sincerely, Alecia Van Atta Assistant Regional Administrator California Coastal Office

Enclosure cc: FRN # 151422WCR2023AR00042 i

Endangered Species Act (ESA) Section 7(a)(2) Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Response

United States Coast Guard Station Humboldt Bay Maintenance Dredging (2023-2032) Project, Humboldt County, California

NMFS Consultation Number: WCRO-2023-00135

Action Agency: United States Coast Guard, Civil Engineering Unit Oakland

Table 1. Affected Species and NMFS' Determinations:

ESA-Listed Species Status

Is Action Likely to Adversely

Affect Species or Critical Habitat?

Is Action Likely to

Jeopardize the Species?

Is Action Likely to Destroy or

Adversely Modify Critical Habitat?

Southern Oregon/Northern California Coast (SONCC) coho salmon

Threatened Yes No No

California Coastal (CC) Chinook salmon Threatened Yes No No

Northern California (NC) steelhead Threatened Yes No No

Southern DPS North American Green Sturgeon Threatened Yes No No

Table 2. Essential Fish Habitat and NMFS' Determinations:

Fishery Management Plan with EFH in the Action Area

Does Action Have an Adverse Effect on EFH?

Are EFH Conservation Recommendations Provided?

Pacific Coast Salmon Yes Yes Pacific Coast Groundfish Yes Yes Coastal Pelagic Species Yes Yes

Consultation Conducted By: National Marine Fisheries Service, West Coast Region

Issued By:

Alecia Van Atta Assistant Regional Administrator California Coastal Office

Date: April 6, 2023 ii

Table of Contents

1 INTRODUCTION

1.1 Background

1.2 Consultation History

1.3 Proposed Federal Action

1.3.1 Project Description

1.3.2 Sediment Suitability and Disposal

1.3.3 Eelgrass Mitigation Plan

1.3.4 Minimization Measures

1.3.5 Other Activities

2 ENDANGERED SPECIES ACT: BIOLOGICAL OPINION AND INCIDENTAL TAKE

STATEMENT

2.1 Analytical Approach

2.2 Rangewide Status of the Species and Critical Habitat

2.2.1 Species Description and General Life History

2.2.2 Status of Species and Critical Habitat

2.2.3 Factors Responsible for the Decline of Species and Critical Habitat

2.3 Action Area

2.4 Environmental Baseline

2.4.1 Status of Listed Species and Critical Habitat in the Action Area

2.4.2 Previous ESA Section 7 Consultations in the Action Area

2.5 Effects of the Action

2.5.1 Propeller and Vessel Strikes

2.5.2 Turbidity

2.5.3 Entrainment

2.5.4 Disposal

2.5.5 Reductions in Prey

2.5.6 Acoustics and Noise

2.5.7 Effects to Critical Habitat

2.6 Cumulative Effects

2.7 Integration and Synthesis

2.8 Conclusion

2.9 Incidental Take Statement

iii

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 Essential Fish Habitat Conservation Recommendations

3.4 Statutory Response Requirement

3.5 Supplemental Consultation

4 DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION REVIEW 27

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

NOAA’s National Marine Fisheries Service (NMFS) prepared the biological opinion (opinion) 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 Part 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 within two weeks at the NOAA Library Institutional Repository [https://repository.library.noaa.gov/welcome]. A complete record of this consultation is on file at the NMFS Northern California Office in Arcata, California.

1.2 Consultation History

On July 5, 2022, the U.S. District Court for the Northern District of California issued an order vacating the 2019 regulations that were revised or added to 50 CFR part 402 in 2019 (“2019 Regulations,” see 84 FR 44976, August 27, 2019) without making a finding on the merits. On September 21, 2022, the U.S. Court of Appeals for the Ninth Circuit granted a temporary stay of the district court’s July 5 order. On November 14, 2022, the Northern District of California issued an order granting the government’s request for voluntary remand without vacating the 2019 regulations. The District Court issued a slightly amended order two days later on November 16, 2022. As a result, the 2019 regulations remain in effect, and we are applying the 2019 regulations here. For purposes of this consultation and in an abundance of caution, we considered whether the substantive analysis and conclusions articulated in the biological opinion and incidental take statement would be any different under the pre-2019 regulations. We have determined that our analysis and conclusions would not be any different.

On January 30, 2023, NMFS received the United States Coast Guard’s (USCG) request for formal ESA consultation, and for EFH consultation, regarding the USCG Station Humboldt Bay Maintenance Dredging (2023-2032) Project. The USCG anticipated adverse effects to Southern Oregon/Northern California Coast (SONCC) coho salmon, California Coastal (CC) Chinook salmon, Northern California (NC) steelhead, Southern Distinct Population Segment (SDPS) of North American green sturgeon and their designated critical habitats. The USCG determined the Project may adversely affect EFH designated by the Pacific Coast Salmon Fishery Management Plan (FMP), Pacific Coast Groundfish FMP, and Coastal Pelagic Species FMP. Formal ESA https://repository.library.noaa.gov/welcome consultation for the Project was initiated upon receipt of the request from the USCG, on January 30, 2023, as well as consultation for EFH.

On March 16, 2023, the USCG provided an update to their proposed action to: (1) remove the potential use of fish screens when hydraulic or suction dredging; and (2) to include an eelgrass mitigation plan in the event any existing eelgrass in the dredge footprint is affected.

1.3 Proposed Federal Action

Under the ESA, “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). Under the MSA, “Federal action” means any action authorized, funded, or undertaken, or proposed to be authorized, funded, or undertaken by a Federal Agency (see 50 CFR 600.910).

The USCG proposes to conduct maintenance dredging of the boat basin at USCG Station Humboldt Bay (Station). In order for the boat basin to remain in operation, sediment removal must be conducted to accommodate the draft of the USCG vessels operating from the basin. The purpose of the project is to maintain functioning boat maneuvering depths at the station to permit the USCG to continue to fulfill its mission.

1.3.1 Project Description

The scope of the proposed project includes dredging and disposal of sediment from within the vessel mooring basin at Station Humboldt Bay (Figure 1). The first maintenance dredge event is proposed to be implemented in 2023 during the proposed in-water work window (July 1 to October 15), with maintenance dredging in subsequent years as needed to maintain operational depth over a 10-year period (2023-2032). Dredging will return the mooring basin area at Station Humboldt Bay to its previously dredged depth of -8 feet below the mean lower low-water (MLLW) mark, plus an additional two feet of over-depth allowance, for a maximum depth of -10 feet MLLW. The total project footprint for maintenance dredging is approximately 0.77 acres.

The total volume to be removed is approximately 3,000 cy of sediment for the first event (2023) with maintenance dredging events in subsequent years expected to remove similar volume amounts. Sloping will occur out to the dredge footprint peripheral extent at a ratio of 2 feet horizontal to 1 foot vertical (2:1). Over the 10-year course of the project, the estimated dredge volume is approximately 10,000 cy. Dredging is anticipated to be performed every three to five years, as needed.

Dredging is anticipated to take approximately one to two weeks to complete. Either mechanical or hydraulic dredging methods may be used. Dredging would be performed from a shallow draft barge equipped with either a crane or excavator clamshell (mechanical dredging) or a suction head (hydraulic dredging). For dredging in and around existing structures, it is anticipated hydraulic dredging may be required.

1.3.1.1 Hydraulic Dredging

If hydraulic dredging is utilized, a temporary dredge pipeline will be assembled to facilitate transport of dredged material to a barge. The dredge pipe diameter may vary depending on the equipment used, but anticipated to be less than 12-inches in diameter. The pipe will be constructed by the contractor in accordance with the specifications for the equipment in a way that would seal the pipe and prevent spills or leakage.

The pipe would connect to a barge that would be anchored nearby the dredging area but outside of (avoiding) any environmentally sensitive areas. The pipe and barge would also be positioned to not obstruct the Federal Navigation Channel (FNC) and still allow access for the USCG to perform regular activities. The contractor may decide to use a floating pipe or anchor or tie equipment to the breakwater to support the pipe without anchoring in the sediment, in which case no additional environmental impacts are expected. The time to assemble and deconstruct the pipe is estimated to be approximately 1-2 weeks.

Figure 1: USCG Station Humboldt Bay overview of dredging footprint (red outline).

1.3.2 Sediment Suitability and Disposal

A sediment characterization study would be performed for all dredging events performed during the 10-year permit cycle. Dredge material placed in the barge would likely be transported by a tugboat directly to the preapproved in-water disposal site at the HOODS. If upland disposal is pursued for the project for future dredging episodes, then Best Management Practices (BMPs) to stabilize and dewater the dredged material will be implemented prior to transport. Dewatering would be performed by the dredged material contractor in accordance with their dredged material management plan. Water generated from the operation would be retained until it meets regional water quality criteria before being discharged into existing storm drains that drain to Humboldt Bay or be pumped back into the bay via a pipeline. Discharges would be monitored to the best extent practicable either through direct water quality monitoring in the bay or by periodic testing of discharge water. The dredged material de-watering process would be designed to prevent any accidental discharge.

1.3.3 Eelgrass Mitigation Plan

If any impacts to the existing eelgrass beds occur, the USCG proposes to transplant eelgrass from existing beds and relocate eelgrass into suitable habitats from where the USCG had removed a marine railway from Humboldt Bay. The planting ratio will occur at a 21:1 ratio to ensure the target of 1.2:1 is achieved. The areas planted will be monitored for five years in adherence with CEMP. If the transplanted eelgrass achieves or surpasses the objective of 1.2:1, the mitigation for eelgrass would be considered to cover eelgrass impacted within the Station in perpetuity.

1.3.4 Minimization Measures

The USCG proposes to incorporate the following conservation measures to minimize the effects of the project:

• All work will occur during the in-water work window (July 1 – October 15).

• A pre-dredging eelgrass (Zostera marina and Zostera pacifica) survey will be conducted during the growing season, and up to a week prior to the start of each dredging episode.

• Best management practices would be employed to prevent impacts on two small clusters of eelgrass totaling 8 square-meters (m2) of vegetated cover, of which approximately 4.8 m2 are within the USCG’s permitted dredging area for long-term maintenance.

• Eelgrass mitigation plans have been developed to reconcile any effects to eelgrass.

• If a silt curtain cannot be deployed, light monitoring shall be conducted by the

Contractor in accordance with light monitoring protocol.

• Vessel operators will follow designated speed zones to and from the project area.

• The potential for grounding will be limited by controlling contractor vessel draft and movements.

• During transport and handling of sediment, containment measures will be used to minimize spillage.

• The USCG will require the contractor to conduct a surface debris survey prior to dredging.

• If needed during offloading, metal spill aprons, upland spill control curbing and collection systems, and other spill control measures will be implemented. If a bucket is used, a dribble apron will be used.

• The contractor will use a Global Positioning System unit to ensure that material is removed from the correct locations.

• The contractor will not be allowed to excavate beyond the maximum authorized depth.

• No bottom stockpiling or multiple bites of the clamshell bucket will be allowed.

• Over-dredging at the base of a slope will not occur.

• If mechanical dredging is employed, the dredge bucket will not be overfilled. The dredge bucket will swing directly to the barge after it breaks the water surface using the minimal swing distance.

• The dump barge will be filled to no more than 80 percent capacity to prevent spillage during transport.

• Although not anticipated to be necessary, surface booms, oil-absorbent pads, and similar materials will be onsite to contain any sheen that may occur on the surface of the water during dredging.

• A debris boom will be installed during in-water construction. Any debris accidentally discharged into the water will be collected, transported to, and disposed of, at an appropriate upland disposal site, or recycled, if appropriate.

• The contractor shall utilize only clean construction materials suitable for use in the aquatic environment.

• The contractor shall ensure no debris, soil, silt, sand, sawdust, rubbish, cement or concrete washings thereof, oil or petroleum products, from construction shall be allowed to enter into or be placed where it may be washed by rainfall or runoff into waters.

• Upon completion of the project the contractor shall completely remove any and all excess material or debris from the work area and recycle or dispose of these materials in an appropriate upland location.

• No re-fueling of equipment shall occur where it could enter waters of the United States.

• Dredging will be completed to a stable slope to maintain the integrity of the riprap-armored banks.

The USCG proposes the following additional measures to be implemented if hydraulic dredging is used to conduct maintenance dredging:

• Limit all priming, clearing, and pumping of water into the cutterhead within three feet of the bottom to minimize impacts on fish.

• Priming and clearing of the cutterhead shall last no longer than five minutes.

• Monitor cutterhead intakes so that they maintain contact with the Bay floor during suction dredging.

• The suction dredge will not be operating while in the water column to minimize entrainment of sensitive species within the water column.

• Overflow to the hopper will be minimized to reduce turbidity in the surrounding waters in Humboldt Bay.

• Entrainment monitoring: California Department of Fish and Wildlife (CDFW) recommends entrainment monitoring to occur during active hydraulic dredging events in Humboldt Bay to determine if BMPs are successful.

1.3.5 Other Activities

We considered whether or not the proposed action would cause any other activities and determined that although the proposed Project will help maintain existing navigation channels, future implementation of the Project will not increase the number of vessel transits per day, vessel size, or other maritime activities in the action area for the foreseeable future because the Project does not include any additional dredging for new or expanded maritime facilities.

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 reasonable and prudent measures (RPMs) and terms and conditions to minimize such impacts.

2.1 Analytical Approach

This biological opinion includes both a jeopardy analysis and 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 biological opinion also relies on the regulatory definition of “destruction or adverse modification,” which “means a direct or indirect alteration that appreciably diminishes the value of critical habitat as a whole for the conservation of a listed species” (50 CFR 402.02). The designations of critical habitat use the term primary constituent element (PCE) or essential features. The 2016 final rule (81 FR 7414; February 11, 2016) that revised the critical habitat regulations (50 CFR 424.12) replaced 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 biological opinion, we use the term PBF to mean PCE or essential feature, as appropriate for the specific critical habitat.

The ESA Section 7 implementing regulations define effects of the action using the term “consequences” (50 CFR 402.02). As explained in the preamble to the final rule revising the definition and adding this term (84 FR 44976, 44977; August 27, 2019), that revision does not change the scope of our analysis, and in this opinion, we use the terms “effects” and “consequences” interchangeably.

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

● Evaluate the rangewide status of the species and critical habitat expected to be adversely affected by the proposed action.

● Evaluate the environmental baseline of the species and critical habitat.

● Evaluate the effects of the proposed action on species and their habitat using an exposure-response approach.

● Evaluate cumulative effects.

● In the integration and synthesis, add the effects of the action and cumulative effects to the environmental baseline, and, in light of the status of the species and critical habitat, analyze whether the proposed action is likely to: (1) directly or indirectly 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, or (2) directly or indirectly result in an alteration that appreciably diminishes the value of critical habitat as a whole for the conservation of a listed species.

● If necessary, suggest a reasonable and prudent alternative to the proposed action.

2.2 Rangewide Status of the Species and Critical Habitat

This opinion examines the status of each species that is likely to 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’ “reproduction, numbers, or distribution” for the jeopardy analysis. The opinion 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 function of the PBFs that are essential for the conservation of the species.

2.2.1 Species Description and General Life History

2.2.1.1 SONCC Coho Salmon

Coho salmon have a generally simple 3‐year life history. The adults typically migrate from the ocean and into bays and estuaries towards their freshwater spawning grounds in late summer and fall, and spawn by mid-winter. Adults die after spawning. The eggs are buried in nests, called redds, in the rivers and streams where the adults spawn. The eggs incubate in the gravel until fish hatch and emerge from the gravel the following spring as fry. These 0+ age fish typically rear in freshwater for about 15 months before migrating to the ocean. The juveniles go through a physiological change during the transition from fresh to salt water called smoltification. Coho salmon smolts typically outmigrate between March and July (Ricker et al. 2014). Coho salmon typically rear in the ocean for two growing seasons, returning to their natal streams as 3‐year-old fish to renew the cycle.

2.2.1.2 CC Chinook Salmon

CC Chinook salmon are typically fall spawners, returning to bays and estuaries before entering their natal streams in the early fall. The adults tend to spawn in the mainstem or larger tributaries of rivers. As with the other anadromous salmon, the eggs are deposited in redds for incubation.

When the 0+ age fish emerge from the gravel in the spring, they typically migrate to saltwater shortly after emergence. Therefore, Chinook salmon typically enter the estuary as smaller fish compared to coho salmon. Chinook salmon are typically present in the stream‐estuary ecotone, which is located in the downstream portions of major tributaries to estuaries like Humboldt Bay, from early May to early September, with peak abundance in June/July (Wallace and Allen 2007).

Similar to coho salmon, prey resources during out-migration are critical to Chinook salmon survival as they grow and move out to the open ocean.

2.2.1.3 NC Steelhead

Steelhead are the anadromous form of O. mykiss, spending time in both fresh and saltwater.

Steelhead generally return to freshwater to spawn as 4 or 5-year-old adults. Unlike other Pacific salmonids, steelhead can survive spawning and return to the ocean only to return to spawn in a future year. It is rare for steelhead to survive more than two spawning cycles. Steelhead typically spawn between December and May. Like other Pacific salmonids, the steelhead female deposits her eggs in a redd for incubation. The 0+ age fish emerge from the gravel to begin their freshwater life stage and can rear in their natal stream for 1 to 4 years before migrating to the ocean.

Steelhead have a similar life history as noted above for coho salmon, in the sense that they rear in freshwater for an extended period before migrating to saltwater. As such, they enter the estuary as larger fish (mean size of about 170 to 180 mm or 6.5 to 7.0 inches) and are, therefore, more oriented to deeper water channels. The California Department of Fish and Wildlife (CDFW) data indicate that steelhead smolts generally migrate downstream toward the estuary between March 1 and July 1 each year, although they have been observed as late as September (Ricker et al. 2014). The peak of the outmigration timing varies from year to year within this range, and generally falls between early April and mid‐May.

2.2.1.4 SDPS Green Sturgeon

Subadult and adult green sturgeon move between coastal waters and estuaries. Lindley et al.

(2011) report multiple rivers and estuaries are visited by aggregations of green sturgeon in summer months, and larger estuaries (e.g., the action area in Humboldt Bay) appear to be particularly important habitat. During the winter months, green sturgeon generally reside in the coastal ocean. Subadult green sturgeon spend several years at sea before reaching reproductive maturity and returning to freshwater to spawn for the first time (Nakamoto et al. 1995).

Juvenile Southern DPS green sturgeon rear in their natal streams in California’s Central Valley, so only sub-adult and adult Southern DPS green sturgeon are present in the marine environment offshore of, and inside of, Humboldt Bay and are the only life stages of Southern DPS green sturgeon that could be present. Sub-adults range from 65-150 cm total length from first ocean entry to size at sexual maturity. Sexually mature adults range from 150-250 cm total length.

2.2.2 Status of Species and Critical Habitat

In this biological opinion, NMFS assesses four population viability parameters to help us understand the status of each species and their ability to survive and recover. These population viability parameters are: abundance, population productivity, spatial structure, and diversity (McElhaney et al. 2000). While there is insufficient information to evaluate these population viability parameters in a thorough quantitative sense, NMFS has used existing information, including the Recovery Plan for SONCC Coho Salmon (NMFS 2014) and Coastal Multispecies Recovery Plan (NMFS 2016), to determine the general condition of each population and factors responsible for the current status of each Evolutionarily Significant Unit (ESU). We use these population viability parameters as surrogates for numbers, reproduction, and distribution, the criteria found within the regulatory definition of jeopardy (50 CFR 402.02).

2.2.2.1 Status of SONCC Coho Salmon

SONCC Coho Salmon Abundance and Productivity: Although long-term data on coho salmon abundance are scarce, the available evidence from short-term research and monitoring efforts indicate that spawner abundance has declined since the last status review for populations in this ESU (Williams et al. 2016). In fact, 24 of the 31 independent populations in the ESU are at high risk of extinction because they are below or likely below their depensation threshold, which can be thought of as the minimum number of adults needed for survival of a population. No populations are at a low risk of extinction and all core populations are thousands short of the numbers needed for recovery (Williams et al. 2016).

SONCC Coho Salmon Spatial Structure and Diversity: The distribution of SONCC coho salmon within the ESU is reduced and fragmented, as evidenced by an increasing number of previously occupied streams from which SONCC coho salmon are now absent (NMFS 2001, Good et al.

2005, Williams et al. 2011, Williams et al. 2016). Extant populations can still be found in all major river basins within the ESU (70 FR 37160; June 28, 2005). However, extirpations, loss of brood years, and sharp declines in abundance (in some cases to zero) of SONCC coho salmon in several streams throughout the ESU indicate that the SONCC coho salmon's spatial structure is more fragmented at the population-level than at the ESU scale. The genetic and life history diversity of populations of SONCC coho salmon is likely very low. The SONCC coho salmon ESU is currently considered likely to become endangered within the foreseeable future in all or a significant portion of its range, and there is heightened risk to the persistence of the ESU as Viable Salmonid Population parameters continue to decline and no improvements have been noted since the previous status review (Williams et al. 2016).

2.2.2.2 Status of CC Chinook Salmon

CC Chinook Salmon Abundance and Productivity: Low abundance, generally negative trends in abundance, reduced distribution, and profound uncertainty as to risk related to the relative lack of population monitoring in California have contributed to NMFS’ conclusion that CC Chinook salmon are likely to become an endangered species within the foreseeable future throughout all or a significant portion of their range. Where monitoring has occurred, Good et al. (2005) found that historical and current information indicates that CC Chinook salmon populations are depressed. Uncertainty about abundance and natural productivity, and reduced distribution are among the risks facing this ESU. Concerns regarding the lack of population-level estimates of abundance, the loss of populations from one diversity stratum1, as well as poor ocean survival contributed to the conclusion that CC Chinook salmon are likely to become an endangered species in the foreseeable future (Good et al. 2005, Williams et al. 2011, Williams et al. 2016).

CC Chinook Salmon Spatial Structure and Diversity: Williams et al. (2011) found that the loss of representation from one diversity stratum, the loss of the spring-run history type in two diversity substrata, and the diminished connectivity between populations in the northern and southern half of the ESU pose a concern regarding viability for this ESU. Based on consideration of this updated information, Williams et al. (2016) concluded the extinction risk of the CC Chinook salmon ESU has not changed since the last status review. The genetic and life history diversity of

1 A diversity stratum is a grouping of populations that share similar genetic features and live in similar ecological conditions.

populations of CC Chinook salmon is likely very low and is inadequate to contribute to a viable ESU, given the significant reductions in abundance and distribution.

2.2.2.3 Status of NC Steelhead

NC Steelhead Spatial Structure and Diversity: NC steelhead remain broadly distributed throughout their range, with the exception of habitat upstream of dams on both the Mad River and Eel River, which has reduced the extent of available habitat. Extant summer-run steelhead populations exist in Redwood Creek and the Mad, Eel (Middle Fork, Van Duzen), and Mattole rivers. The abundance of summer-run steelhead was considered “very low” in 1996 (Good et al.

2005), indicating that an important component of life history diversity in this DPS is at risk.

Hatchery practices in this DPS have exposed the wild population to genetic introgression and the potential for deleterious interactions between native stock and introduced steelhead. However, abundance and productivity in this DPS are of most concern, relative to NC steelhead spatial structure and diversity (Williams et al. 2011).

NC Steelhead Abundance and Productivity: With few exceptions, NC steelhead are present wherever streams are accessible to anadromous fish and have sufficient flows. The most recent status review by Williams et al. (2016) reports that available information for winter-run and summer-run populations of NC steelhead do not suggest an appreciable increase or decrease in extinction risk since publication of the last viability assessment (Williams et al. 2011). Williams et al. (2016) found that population abundance was very low relative to historical estimates, and recent trends are downwards in most stocks.

2.2.2.4 Status of SDPS Green Sturgeon

SDPS Green Sturgeon Spatial Structure and Diversity: SDPS green sturgeon continue to rely mostly on one portion of one river (Sacramento River) for spawning, and the most recent status review (NMFS 2021) confirms the amount of spawning habitat has not increased. Spawning has occurred episodically in the Feather and Yuba Rivers but it has not been continuous (Beccio 2019). The limited amount of spawning locations inherently limits the spatial structure and diversity for the DPS.

SDPS Green Sturgeon Abundance and Productivity: The recovery criteria established by the SDPS green sturgeon recovery plan (NMFS 2018) is for the adult census population to remain at or above 3,000 for three generations (this equates to a yearly running average of at least 813 spawning adults for approximately 66 years). In addition, the effective population size must be at least 500 individuals in any given year and each annual spawning run must comprise a combined total, from all spawning locations, of at least 500 adult fish in any given year. The estimated total population of Southern DPS green sturgeon is 17,548 individuals, with an estimated 2,106 adults (Mora et al. 2018). The adult population does not meet the criteria of a yearly average 3,000 adults and the reported counts of spawning adults have been less than 500 in the Sacramento River (Mora et al. 2018).

2.2.2.5 Status of Critical Habitats

The condition of SONCC coho salmon, CC Chinook salmon, and NC steelhead critical habitat, specifically its ability to provide for their conservation, has been degraded from conditions known to support viable salmonid populations. NMFS has determined that currently depressed population conditions are, in part, the result of the following human induced factors affecting critical habitat: logging, agriculture, mining, urbanization, stream channelization, dams, wetland loss, and water withdrawals (including unscreened diversions for irrigation). Impacts of concern include altered stream bank and channel morphology, elevated water temperature, lost spawning and rearing habitat, habitat fragmentation, impaired gravel and wood recruitment from upstream sources, degraded water quality, lost riparian vegetation, and increased erosion into streams from upland areas (Williams et al. 2016, Weitkamp et al. 1995). Diversion and storage of river and stream flow has dramatically altered the natural hydrologic cycle in many of the streams within the ESU’s and DPS. Altered flow regimes can delay or preclude migration, dewater aquatic habitat, and strand fish in disconnected pools, while unscreened diversions can entrain juvenile fish.

The current condition of critical habitat for the SDPS green sturgeon is degraded over its historical conditions. It does not provide the full extent of conservation values necessary for the recovery of the species, particularly in the upstream riverine habitat of the Sacramento River.

In the Sacramento River, migration corridor and water flow PBFs have been impacted by human actions, substantially altering the historical river characteristics in which the SDPS of green sturgeon evolved. In addition, the Delta may have a particularly strong impact on the survival and recruitment of juvenile green sturgeon due to their protracted rearing time in brackish and estuarine waters.

The construction of dams, water diversions, flood control projects, agricultural development and resources extraction have contributed to the decline of the SDPS green sturgeon. The SDPS Green Sturgeon Recovery Plan’s priority actions are intended to restore passage and habitat, reduce mortality from fisheries, entrainment, and poaching, and address threats in the areas of contaminants, climate change, predation, sediment loading and oil and chemical spills. Most of the recovery efforts focus on the Sacramento River Basin and San Francisco Bay Delta Estuary environments, as threats in spawning and rearing habitats were considered the greatest impediments to recovery.

2.2.3 Factors Responsible for the Decline of Species and Critical Habitat The factors that caused declines of species and degradation of critical habitat include hatchery practices, ocean conditions, habitat loss due to dam building, degradation of freshwater habitats due to a variety of agricultural and forestry practices, water diversions, urbanization, over-fishing, mining, climate change, and severe flood events exacerbated by land use practices (Good et al. 2005, Williams et al. 2016). Sedimentation and loss of spawning gravels associated with poor forestry practices and road building are particularly chronic problems that can reduce the productivity of salmonid populations. Late 1980s and early 1990s droughts and unfavorable ocean conditions were identified as further likely causes of decreased abundance (Good et al.

2005). From 2014 through 2016, drought conditions in California reduced stream flows and increased temperatures, further exacerbating stress and disease. Ocean conditions have been unfavorable in past years due to the El Niño in 2015 and 2016 and other anomalously warm waters in the Gulf of Alaska. Reduced flows can cause increases in water temperature, resulting in increased heat stress to fish and thermal barriers to migration.

Another factor affecting the range wide status of SONCC coho salmon, CC Chinook salmon and NC steelhead, and aquatic habitat at large is climate change. Recent work by the NMFS Science Centers ranked the relative vulnerability of west-coast salmon and steelhead to climate change.

In California, listed coho and Chinook salmon are generally at greater risk (high to very high risk) than listed steelhead (moderate to high risk) (Crozier et al 2019).

Impacts from global climate change are already occurring in California. For example, average annual air temperatures, heat extremes, and sea level increased in California over the last century (Kadir et al. 2013). Snowmelt from the Sierra Nevada has declined (Kadir et al. 2013). Although SONCC coho salmon, CC Chinook salmon and NC steelhead are not dependent on snowmelt driven streams, they have likely already experienced some detrimental impacts from climate change through lower and more variable stream flows, warmer stream temperatures, and changes in ocean conditions. California experienced well below average precipitation during the 2012- 2016 drought, as well as record high surface air temperatures in 2014 and 2015, and record low snowpack in 2015 (Williams et al. 2016). Paleoclimate reconstructions suggest the 2012-2016 drought was the most extreme in the past 500 to 1000 years (Williams et al. 2016, Williams et al.

2020, Williams et al. 2022). Anomalously high surface temperatures substantially amplified annual water deficits during 2012-2016. California entered another period of drought in 2020.

These drought periods are now likely part of a larger drought event (Williams et al. 2022). This recent long-term drought, as well as the increased incidence and magnitude of wildfires in California, have likely been exacerbated by climate change (Williams et al. 2020, Williams et al.

2022, Williams et al. 2019).

The threat to SONCC coho salmon, CC Chinook salmon, NC steelhead, and SDPS green sturgeon from global climate change is expected to increase in the future. Modeling of climate change impacts in California suggests that average summer air temperatures are expected to continue to increase (Lindley et al. 2007, Moser et al. 2012). Heat waves are expected to occur more often, and heat wave temperatures are likely to be higher (Hayhoe et al. 2004, Moser et al.

2012, Kadir et al. 2013). Total precipitation in California may decline and the magnitude and frequency of dry years may increase (Lindley et al. 2007, Schneider 2007, Moser et al. 2012).

Similarly, wildfires are expected to increase in frequency and magnitude (Westerling et al. 2011, Moser et al. 2012). Increases in wide year-to- year variation in precipitation amounts (droughts and floods) are projected to occur (Swain et al. 2018). Estuarine productivity is likely to change based on changes in freshwater flows, nutrient cycling, and sediment amounts (Scavia et al.

2002, Ruggiero et al. 2010).

In marine environments, ecosystems and habitats important to juvenile and adult salmonids are likely to experience changes in temperatures, circulation, water chemistry, and food supplies (Brewer and Barry 2008, Feely 2004, Osgood 2008, Turley 2008, Abdul-Aziz et al. 2011, Doney et al. 2012). Some of these changes, including an increased incidence of marine heat waves, are likely already occurring, and are expected to increase. In fall 2014, and again in 2019, a marine heatwave, known as “The Blob”2, formed throughout the northeast Pacific Ocean, which greatly affected water temperature and upwelling from the Bering Sea off Alaska, south to the coastline of Mexico. The marine waters in this region of the ocean are utilized by salmonids for foraging as they mature (Beamish 2018). Although the implications of these events on salmonid

2 https://www.fisheries.noaa.gov/feature-story/new-marine-heatwave-emerges-west-coast-resembles-blob populations are not fully understood, they are having considerable adverse consequences to the productivity of these ecosystems and presumably contributing to poor marine survival of salmonids.

Overall, climate change is believed to represent a growing threat, and will challenge the resilience of SONCC coho salmon, CC Chinook salmon, NC steelhead, and SDPS green sturgeon.

2.3 Action Area

“Action area” means all areas to be affected directly or indirectly by the Federal action and not merely the immediate area involved in the action (50 CFR 402.02). The action area for the proposed action includes the USCG Station Humboldt Bay and as far as 500-feet from the Station, as well as the eelgrass mitigation area, and the expanded HOODS including the routes used to transport the dredge material for disposal.

2.4 Environmental Baseline

The “environmental baseline” refers to the condition of the listed species or its designated critical habitat in the action area, without the consequences to the listed species or designated critical habitat caused by the proposed action. The environmental baseline includes the past and present impacts of all Federal, State, or private actions and other human activities in the action area, the anticipated impacts of all proposed Federal projects in the action area that have already undergone formal or early section 7 consultations, and the impact of State or private actions which are contemporaneous with the consultation in process. The consequences to listed species or designated critical habitat from ongoing agency activities or existing agency facilities that are not within the agency’s discretion to modify are part of the environmental baseline (50 CFR 402.02).

In the action area, the threat to SONCC coho salmon, CC Chinook salmon, NC steelhead, and SDPS green sturgeon from climate change are likely to be similar to those described above in the Species Status section. For example, the action area is likely to experience increases in average summer air temperatures; more extreme heat waves; and an increased frequency of drought (Lindley et al. 2007). In addition to the increased frequency of drought, high intensity rainfall events are also expected to become more common, leading to increased erosion and flooding. In future years and decades, many of these changes are likely to further degrade habitat throughout Humboldt Bay by, for example, reducing streamflow entering the bay during the summer and raising summer water temperatures.

Coho salmon occurring in the action area belong to the Humboldt Bay Tributaries population of SONCC coho salmon, which is currently at a moderate risk of extinction (NMFS 2014). Chinook salmon occurring in the action area belong to the Humboldt Bay Tributaries population of CC Chinook salmon (NMFS 2016), which is well below the number needed to be at a low risk of extinction. NC steelhead in the action area belong to the Humboldt Bay Tributaries population of NC steelhead. All of the listed salmonid populations have the same name and encompass all of the tributaries draining into Humboldt Bay. The spatial extent of these populations indicates that fish born in Freshwater Creek (a Humboldt Bay tributary) may return to Humboldt Bay as adults and spawn in any of the Humboldt Bay tributaries, as the entire network of tributaries draining into the bay constitute one population area.

The highest rated threats identified in the recovery plan for SONCC coho salmon include roads, channelization/diking, and agricultural practices (NMFS 2014). The highest rated threats identified in the recovery plan for CC Chinook salmon include roads/railroads and channel modifications such as levees (NMFS 2016). High priority recovery actions in the SONCC Coho Salmon Recovery Plan and the Coastal Multi-Species Recovery Plan (Chinook salmon) are to increase instream structure; construct off channel habitats and oxbows; remove or set back levees; improve grazing practices; and restore tidally influenced areas (NMFS 2014, 2016).

2.4.1 Status of Listed Species and Critical Habitat in the Action Area Freshwater Creek is one of the major tributaries draining into Humboldt Bay and is likely to represent about half of the anadromous habitat within the Bay. Counts of adult salmonids, including SONCC coho salmon and CC Chinook salmon, at the Freshwater Creek weir from 1994 through 2014 indicates that both wild populations have declined (Ricker et al. 2014).

Ricker et al. (2014) characterized the decline in CC Chinook salmon in Freshwater Creek as dramatic, and raised concerns over depensatory population effects. Once the augmentation of hatchery reared Chinook salmon ceased in 2004, weir captures declined rapidly into the single digits and ultimately reached an all-time low of no returning adults in 2013 (Ricker et al. 2014).

Freshwater Creek adult abundance estimates for SONCC coho salmon also indicates that adult escapement has declined, ranging from a high of 1,807 in 2002-03 to a low of 89 in 2009-10 (Moore and Ricker 2012). Information on abundance of winter steelhead in Humboldt Bay is limited, but adult steelhead returning to Freshwater Creek from 2000 to 2014 have ranged from a low of 51 to a high of 432 adults (Ricker et al. 2014).

Salmonids occurring in estuaries are highly mobile and in Humboldt Bay, low numbers of fish are spread over a large area, which can complicate scientific observations or captures intended to understand their habitat preferences (Garwood et al.