19-01-30-WCR-2018-9148-NMFS Biop Sir Francis Drake Blvd Improvement.pdf

January 30, 2019 Refer to NMFS No: WCR-2018-9148

Nathan Allen, Project Manager

Federal Highways Administration

Central Federal Lands Highway Division

12300 West Dakota Avenue, Suite 380A

Lakewood, Colorado 80228-2583

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

Fishery Conservation and Management Act Essential Fish Habitat Response for the Sir

Francis Drake Boulevard Improvement Project, Marin County, California

Dear Mr. Allen:

Thank you for your letter of March 8, 2018, requesting initiation of 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 Sir Francis Drake Boulevard (SFDB)

Improvement Project (Project) within Point Reyes National Seashore (PRNS) in Marin County, California. The Federal Highway Administration Central Federal Lands Highway Division

(FWHA-CFLHD), in cooperation with Marin County and the National Park Service (NPS), proposes to improve Sir Francis Drake Boulevard in order to restore the structural integrity of the road and enhance safety for all users while reducing ongoing maintenance requirements.

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. NMFS has determined that the proposed Project would adversely affect EFH for various federally managed fish species under the Coastal Pelagic and Pacific Groundfish Fishery Management Plans.

The enclosed biological opinion is based on our review of the FWHA-CFLHD description of the

Project, and describes NMFS' analysis of potential effects on threatened Central California Coast

(CCC) steelhead (Oncorhynchus mykiss) and CCC coho salmon (O. kisutch), and their designated critical habitat, in accordance with Section 7 of the ESA. Threatened CCC steelhead are known to utilize habitat within the Project’s action area, however, endangered CCC coho salmon are unlikely to occur. The project area is designated critical habitat for both CCC coho salmon and steelhead.

In the enclosed biological opinion, NMFS concludes the project is not likely to jeopardize the continued existence of threatened CCC steelhead, nor is it likely to adversely modify CCC steelhead or CCC coho salmon critical habitat. However, NMFS is aware that take of CCC steelhead may occur as a result of project construction. NMFS has also found that the proposed

Project is not likely to adversely affect CCC coho in accordance with section 7 of the ESA.

Please contact Sara Azat at 707-575-6067 or sara.azat@noaa.gov if you have any questions concerning this Section 7 consultation, or if you require additional information.

Sincerely, Barry A. Thom

Regional Administrator

Enclosure cc: Federal Highways Administration, Oakland, California

Division File copy 151422WCR2014SR00201

Endangered Species Act (ESA) Section 7(a)(2) Biological Opinion and

Magnuson-Stevens Fishery Conservation and Management Act

Essential Fish Habitat Response

NMFS Consultation Number: WCR-2018-9148

Action Agency: Federal Highways Administration

Table 1. Affected Species and NMFS' Determinations:

ESA-Listed

Species

Status

Is Action

Likely to

Adversely

Affect

Species?

Is Action

Likely To

Jeopardize the Species?

Is Action

Likely to

Adversely

Affect

Critical

Habitat?

Is Action

Likely To

Destroy or

Adversely

Modify Critical

Habitat?

Central

California Coast steelhead

(Oncorhynchus mykiss)

Threatened Yes No Yes No

Central

California Coast

Coho

(O. kisutch)

Endangered No No Yes No

Table 2. Essential Fish Habitat and NMFS' Determinations:

Fishery Management Plan

That Identifies EFH in the

Project Area

Does Action Have an Adverse

Effect on EFH?

Are EFH Conservation

Recommendations Provided?

Pacific Coast Groundfish Yes No

Coastal Pelagic Yes No

Pacific Coast Salmon Yes No

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

Issued By:

Barry A. Thom

Regional Administrator

Date: January 30, 2019

Table of Contents

1 INTRODUCTION

1.1 Background

1.2 Consultation History

1.3 Proposed Federal Action

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 CCC steelhead status

2.2.2 Status of CCC steelhead and CCC coho salmon critical habitat

2.2.3 Additional Threats to the CCC steelhead DPS and Critical Habitat of CCC steelhead and CCC coho salmon

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 Factors Affecting Species Environment within the Action Area

2.4.3 Previous Section 7 Consultations and Section 10 Permits in the Action Area

2.5 Effects of the Action

2.6 Cumulative Effects

2.7 Integration and Synthesis

2.8 Conclusion

2.9 Incidental Take Statement

2.9.1 Amount or Extent of Take

2.9.2 Effect of the Take

2.9.3 Reasonable and Prudent Measures

2.9.4 Terms and Conditions

2.10 Conservation Recommendations

2.11 Reinitiation of Consultation

2.12 “Not Likely to Adversely Affect”’ Determinations

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 Supplemental Consultation

4 DATA QUALITY ACT DOCUMENTATION AND PRE-DISSEMINATION REVIEW 28

4.1 Utility

4.2 Integrity

4.3 Objectivity

5 REFERENCES

5.1 Scientific Literature, Government Reports, and Similar Documents

5.2 Federal Register Notices

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 of 1973 (ESA)(16 USC 1531 et seq.), and implementing regulations at 50 CFR 402.

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

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

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

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

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

Tracking System (PCTS) [PCTS Homepage]. A complete record of this consultation is on file at the NMFS California Coastal Office in Santa Rosa, California.

1.2 Consultation History

Prior to consultation, technical assistance and project information was discussed between NMFS, the Federal Highway Administration Central Federal Lands Highway Division (FWHA-

CFLHD), and Jacobs Consulting (Jacobs) beginning with written correspondence dated June 11, 2014 continuing through January 12, 2015 (Jacobs 2015). On June 16, 2015, NMFS received a concurrence request letter, from FWHA-CFLHD, and a biological assessment (BA), dated May

2015 prepared by Jacobs for FWHA-CFLHD, for the Sir Francis Drake Rehabilitation project.

From July 23, 2015 to December 7, 2017, several interagency meetings and/or phone conferences were held to discuss water quality control measures, best management practices

(BMPs) for avoiding turbidity during culvert replacement, dewatering, erosion control plans, embankment stabilization design at East Schooner Creek, and to provide information and feedback on the project design and progress (Jacobs 2018). FWHA-CFLHD initially determined that the proposed action may affect, but is not likely to adversely affect CCC steelhead, coho, and their critical habitats, and no effect on North American green sturgeon and their critical habitat.

On February 26, 2016, FWHA-CFLHD notified NMFS, via telephone, that they would withdraw the consultation until project design changes could be developed to address potential impacts related to ESA-listed species, critical habitat and EFH. An addendum to the BA was provided to

NMFS on March 8, 2018, with a revised determination that the project may affect CCC steelhead; FWHA-CFLHD determined that although CCC steelhead would not likely to be present between July 1 and October 15 when in-channel work is proposed, the species is known to occur within the Action Area. Additional information on the bank stabilization design was provided by request from NMFS on June 22, 2018.

https://pcts.nmfs.noaa.gov/pcts-web/homepage.pcts

On July 26, 2018, NMFS, FWHA-CFLHD and Jacobs met, via teleconference, to discuss remaining questions regarding the critical habitat effects determination, the proposed wetland mitigation design and monitoring, and any potential changes to the project description pending the San Francisco Bay Regional Water Quality Control Board (SFBRWQCB) comments submitted to FWHA-CFLHD on July 24, 2018. It was agreed that project changes resulting from

FWHA-CFLHD meeting with SFBRWQCB would be forwarded to NMFS when finalized. No project changes resulted from the SFBRWQCB, FWHA-CFLHD responded to the comment letter via email on November 8, 2018. The final project description was confirmed September

14, 2018.

1.3 Proposed Federal Action

“Action” means all activities or programs of any kind authorized, funded, or carried out, in whole or in part, by Federal agencies (50 CFR 402.02). The proposed action by FWHA-CFLHD will modernize Sir Francis Drake Boulevard (SFDB) within Point Reyes National Seashore

(PRNS) in Marin County California. The portion of SFDB within PRNS is an old wagon road that has been improved with chip seals and overlays. The roadway is within a 60-foot wide

Marin County easement extending for approximately 12 miles within PRNS, from Pierce Point

Road to Chimney Rock Road and Lighthouse Road; the road provides the only means of vehicular park-visitor access to several other popular recreational destinations and is also used by the local ranching and residential community. The existing pavement was not designed for current traffic loads and is damaged and rapidly deteriorating.

Seasonal flooding of SFDB near crossings of Schooner Creek and East Schooner Creek can close the road for several days annually. The road’s current deteriorated state requires significant ongoing maintenance, which will be substantially reduced if rehabilitated. To compensate for permanent impacts as a result of roadway improvements, FWHA-CFLHD has proposed construction of a wetland mitigation site at Drakes Beach. The proposed mitigation would remove existing pavement and soil to facilitate the re-establishment of a historic wetland.

The proposed project includes resurfacing, restoration, and rehabilitation that will closely follow the existing roadway (Figure 1). New asphalt pavement, new striping and signs, replacement of two cattle under-crossings, replacement of cross culverts from multiple roadside drainage ditches with larger culverts, replacement of two stream crossings, and implementation of other features to meet current design standards are proposed. The road could be widened between one and six feet in some areas to create a consistent width and to improve safety; however, widening would be kept to a minimum to avoid and minimize impacts to adjacent sensitive resources. The proposed improvements would generally occur within the 60-foot wide Marin County roadway easement. In a few locations, proposed improvements may extend slightly beyond the existing easement to improve sight distance and safety, accommodate widening in areas of steep slopes, and to reduce scour and flood risk near the Schooner Creek and East Schooner Creek crossings.

The two roadway stream crossing replacements, at Schooner Creek and East Schooner Creek where flooding occurs, are within designated critical habitat for Central California Coast (CCC) steelhead and CCC coho salmon. Proposed activities which could directly affect these species and critical habitat include roadway work, vegetation removal and soil disturbance, sediment removal, culvert removal/replacement and bridge installation, and in-channel work to restore channel capacity and/or protect the crossings from scour at high flows. All work within the creek channels would occur between July 1 and October 15.

Schooner Creek. Proposed work at the Schooner Creek crossing would include replacing two 7-foot diameter culverts within the tidal section of Schooner Creek with a 57-foot long, single-span bridge. The existing two culverts of the current crossing do not meet NMFS fish passage guidelines, and partially function as a dam, particularly at high tide, causing increased tidal velocities which likely result in salinity stratification and poor rearing conditions for young of the year salmonids. Removal of the two culverts and installation of the proposed bridge would occur in two phases in order to continue traffic on the roadway. Both phases include the same actions, first on the upstream side of the creek, and then on the downstream side. Shallow trenches will be excavated within existing road fill at the bridge abutment locations to drill the caissons and pour the abutment cap. The existing roadway fill would serve as berms for this construction to provide dry working areas at each abutment, with a small manmade berm required at the southwest corner of the bridge where the bridge abutment is higher than the existing fill. An excavator would be used in the middle of the Schooner Creek channel in order to remove the existing road fill and half of the culverts during each phase. Ordinary stream flows could be maintained through the work zone by diverting channel flows into one of the 84-inch culverts or a temporary flexible plastic corrugated pipe the length of the work zone. Some in-channel work would occur on the upstream and downstream sides of the creek for minor channel shaping and to install riprap for bridge abutment scour protection prior to placing bridge beams and decking during each phase. No piling driving is proposed. Flows would be maintained during construction of the bridge foundations and isolated from work zone during placement of riprap for abutment protection. During construction and installation of the bridge, the width of the channel would remain the same or larger, which would temporarily alter aquatic habitat. The estuarine width at high tide, post-construction, would be approximately 50 feet, 36 feet wider than the current dimension. Work within Schooner Creek would be scheduled during low tides.

East Schooner Creek. Work within East Schooner Creek will address erosion of the roadway and embankment into East Schooner Creek. The creek channel width, within proposed work locations, varies between 4 and 12 feet, and water depth is approximately 18-24 inches.

Presently, the eroding roadway is degrading aquatic habitat and water quality conditions through deposition of eroded sediment and there is a risk of road failure. To restore and stabilize the roadway, approximately 710 linear feet (5,680 square feet) of biotechnical bank stabilization would be installed to re-establish the roadway embankment in this area. Based on agency coordination and input, the roadside embankment would be constructed of rock with willow and salvaged native plants. A rock and geotextile rock wall foundation is intended to facilitate drainage, and buried riprap at the toe of slope is expected to further prevent scouring.

The intent of the bank stabilization design is to maintain the channel in its current location.

However, the design is dependent on hydraulic and geotechnical analyses and it is possible that the design may be unable to achieve a 1.5:1 or steeper slope face while also ensuring integrity of the roadway. For this reason, it is possible that a portion or the entirety of the project length (710 feet, approximately 5,680 square feet) of the East Schooner Creek channel may be shifted 6–8 feet east-southeast away from the roadway. In some areas, there is an existing buffer between the creek bed and roadway to allow for isolation of the work zone from the creek; some areas of the roadway are already uncut by the creek and will need to be shifted. This exact area will not be known until construction begins. A qualified biologist shall monitor the construction site during placement and removal of channel diversions and cofferdams to ensure than adverse effects to salmonids are minimized.

The proposed work also includes replacement of an existing culvert with a box culvert at the crossing of Sir Francis Drake Boulevard and East Schooner Creek. The existing 84-inch by 50-inch corrugated metal pipe culvert would be replaced with a new concrete box culvert with a maximum height of 6 feet high and 12 feet wide. Installation of the new box culvert would require the excavation of an estimated 54 cubic yards of sediment 27 feet up-and 62 feet downstream of the crossing, clearing and grubbing of vegetation to approximately 8 feet, as well as installation of a new 12-in wide cast-in-place concrete headwall and concrete toe wall.

Mitigation. To compensate for permanent wetland impacts as a result of roadway improvements, construction of a wetland mitigation site is proposed at the Drakes Beach parking lot.

Construction of the parking lot in the 1950s and 1960s resulted in filling a large wetland adjacent to Drakes Beach. The proposed mitigation would remove approximately half of the existing parking lot (approximately 2 acres) in an effort to re-establish the historic wetland. The parking lot would be reconfigured from 399 spaces to 314 spaces. Surrounding upland areas would also be excavated to expand the mitigation site. Based on the conceptual design, total wetland creation is anticipated to be approximately 2 acres of freshwater wetland with brackish components (Figure 2).

The work to create the wetland would consist of removing the existing pavement and approximately 2–4 feet of the underlying soil. Removal of this upper soil layer would help to eliminate any materials or toxins that may have leached from the parking lot surface. After removal of this soil, compaction within the site would likely have to be reduced through the use of heavy equipment such as scrapers, dozers with rippers, and/or trackhoe excavators. Once compaction is addressed and preliminary construction elevation obtained, final grading with incorporation of organic matter will be necessary. Finished elevations will be based upon hydraulics for the site based upon field monitoring of ground water elevations, analysis of

National Oceanic and Atmospheric Administration (NOAA) tidal gauges, and updated field survey data.

The sanitary sewer line, which is currently located below the asphalt segment of the Peter Behr

Overlook Trail between Drakes Beach and the parking lot, would be lowered in place to facilitate restoration activities. The footpath, which leads to the scenic overlook trailhead, would be maintained for access to the overlook but the asphalt between the visitor center and trailhead would be removed to facilitate restoration to a more natural dune. Fencing, consisting of pins and poles, may be placed along the trail alignment to guide visitors to the trailhead. In addition, there are three existing 24-inch corrugated metal pipe culverts located at the southern tip of the parking lot through which an unnamed intermittent stream flows into Drakes Bay. These culverts are proposed to be removed and the beach head lowered to an elevation that achieves desired wetland mitigation acreage and function while allowing for tidal influence and interaction upon the wetland over time.

In addition to the wetland mitigation, two ponds would be constructed on Home Ranch, within

PRNS, for the purposes of providing aquatic breeding habitat for California red-legged frogs, a threatened species under the ESA, and to compensate for wetland impacts. A hydrologic, hydraulic and ecologic functions monitoring plan has been submitted to the SFBRWQCB.

Figure 1. Project Location

Figure 2. Wetland Mitigation Overview

Best Management Practices and Minimization Measures. A complete list of standard, as well as project specific, best practices and avoidance and minimization measures is listed in Appendix C of the biological assessment addendum (Jacobs 2018). Excerpted from Appendix C are those listed below which will minimize or avoid impacts to listed salmonids:

For all activities occurring within the bed or bank of a drainage, daily construction monitoring by a qualified biologist shall be required.

Any dewatering using pumps shall include screening not to exceed 0.2 inch mesh size. Pump intakes shall be placed in larger, perforated intake basins to allow water to be drawn into the pump while protecting aquatic organisms from entrainment.

Both the outside of the intake basin and the pump intake shall be screened. The perforated intake basin shall be large enough to reduce the intake velocity so as not to impinge aquatic organisms on the screen.

Impacts to overhanging riparian vegetation will be minimized to the maximum extent practicable to reduce loss of shading and structure along East Schooner

Creek and other wetlands and waterways while allowing equipment access to the waterbodies.

Removal of large woody debris shall be limited to the area necessary to complete excavation and rock placement.

The area beyond the construction limits shall not be disturbed. Abandoned segments of roadway and temporary impact areas along SFDB within the project limits that would no longer be in use shall be reclaimed and revegetated. Degraded areas impacted from construction-related activity shall be replanted with native plants from the watershed or nearby watershed under guidance from PRNS biologists. Shrubs, trees, and herbaceous perennials and annuals shall be seeded and planted along riparian corridors where impacts and vegetation removal occur.

CFLHD shall prepare a restoration plan for the project in consultation with PRNS for appropriate seed mixes and plants. Revegetated areas shall be protected and cared for, including watering when needed, until restoration criteria have been met under U.S. Army Corps of Engineers (USACE) permits, the U.S. Fish and Wildlife

Service (USFWS) Biological Opinion, or National Pollutant Discharge Elimination

System (NPDES) standards. Revegetated areas shall be monitored in accordance with an approved restoration plan to ensure success criteria are met.

Work in Schooner Creek, East Schooner Creek, and unnamed drainages between project mile (PM) 9 and PM 12 shall be conducted during no- to low-flow periods of the year (July 1 to October 15 or the first significant fall rainfall; i.e., 0.2 inches over a 24-hour period). For the remainder of the project corridor, culvert repair or replacement and associated work shall be completed during the dry season— typically between April 15 and October 15 or the first significant fall rainfall. All construction-related work within waterways that cross the project area shall be done in accordance with permit conditions.

Concrete and asphalt piles shall be stockpiled outside and away from wetland resource areas, surrounded with fiber rolls, and covered with plastic.

Temporarily impacted wetlands shall be restored on-site to pre-construction conditions through planting vegetation and hydroseeding with a local, native seed mix.

CFLHD shall compensate for permanent loss of jurisdictional features through creation of wetland and riparian compensatory mitigation. The replacement ratio will be 1.5:1 (acres replaced to acres impacted) or as negotiated with regulatory agencies, in accordance with permit terms and conditions. A mitigation and monitoring plan shall be developed for on-site restoration of temporarily impacted wetlands and riparian habitat, restoration or mitigation of permanently impacted riparian habitat, and mitigation of permanently impacted wetlands.

CFLHD shall comply with the California Stormwater BMP Handbook (2009), specifically addressing procedures for the proper use, storage, and disposal of materials and equipment on temporary construction pads to minimize or eliminate the discharge of potential pollutants to a watercourse (NS-14 in handbook). CFLHD shall also comply with procedures to protect waterbodies from debris and wastes associated with structure demolition or removal over or adjacent to watercourses

(NS-15 in handbook).

All materials placed in watercourses shall be nontoxic. Any combination of wood, plastic, cured concrete, steel pilings, or other materials used for in-channel structures shall not contain coatings or treatments, or consist of substances deleterious to aquatic organism that may leach into the surrounding environment in amounts harmful to aquatic organisms.

Construction at Drakes Beach parking lot will not occur during the seasonal beach closures (typically January–March) along Drakes Beach as established yearly by the

NPS. The Contracting Officer’s Engineer will coordinate with NPS and notify contractor when construction may begin.

2 ENDANGERED SPECIES ACT: BIOLOGICAL OPINION AND INCIDENTAL

TAKE STATEMENT

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

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

The FWHA-CFLHD determined the proposed action is not likely to adversely affect CCC steelhead critical habitat, or CCO coho salmon and their critical habitat. Our concurrence with the determination for CCC coho salmon is documented in the "Not Likely to Adversely Affect"

Determinations section 2.11 of this opinion. This opinion discusses the potential adverse effects to CCC steelhead, and CCC steelhead and CCC coho salmon critical habitats.

CCC coho salmon and CCC steelhead critical habitat occur within the action area, and CCC steelhead inhabit Schooner Creek and East Schooner Creek, in the action area, when suitable streamflow exists.

2.1 Analytical Approach

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

(50 CFR 402.02). Therefore, the jeopardy analysis considers both survival and recovery of the species.

This biological opinion relies on the definition of "destruction or adverse modification," which

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

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

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

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

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

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

Describe the environmental baseline in the action area.

Analyze the effects of the proposed action on both species and their habitat using an

“exposure-response-risk” approach.

Describe any cumulative effects in the action area.

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

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

If necessary, suggest a RPA to the proposed action.

2.2 Rangewide Status of the Species and Critical Habitat

This opinion examines the status of each species that would be adversely affected by the proposed action. The status is determined by the level of extinction risk that the listed species face, based on parameters considered in documents such as recovery plans, status reviews, and listing decisions. This informs the description of the species’ likelihood of both survival and recovery. The species status section also helps to inform the description of the species’ current

“reproduction, numbers, or distribution” as described in 50 CFR 402.02. The 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 current function of the essential PBFs that help to form that conservation value.

This biological opinion analyzes the effects of the action on the following listed salmonids and critical habitat:

i. Threatened CCC steelhead Distinct Population Segment (DPS)

Listing determination (71 FR 834; January 5, 2006)

Critical habitat designation (70 FR 52488; September 2, 2005);

ii. Endangered CCC coho salmon Evolutionarily Significant Unit (ESU)

Critical habitat designation (64 FR 24049; May 5, 1999).

2.2.1 CCC steelhead status

Historically, approximately 70 populations1 of steelhead existed in the CCC steelhead DPS

(Spence et al. 2008, Spence et al. 2012). Many of these populations (about 37) were independent, or potentially independent, meaning they had a high likelihood of surviving for 100 years absent anthropogenic impacts (Bjorkstedt et al. 2005). The remaining populations were dependent upon immigration from nearby CCC steelhead DPS populations to ensure their viability (McElhaney et al. 2000, Bjorkstedt et al. 2005).

While historical and present data on abundance are limited, CCC steelhead numbers are substantially reduced from historical levels. A total of 94,000 adult steelhead were estimated to spawn in the rivers of this DPS in the mid-1960s, including 50,000 fish in the Russian River - the largest population within the DPS (Busby et al. 1996). Recent estimates for the Russian River are on the order of 4,000 fish (NMFS 1997). Abundance estimates for smaller coastal streams in the DPS indicate low but stable levels with recent estimates for several streams (Lagunitas, Waddell, Scott, San Vicente, Pudding, and Caspar creeks) of individual run sizes of 500 fish or less (62 FR 43937). Some loss of genetic diversity has been documented and attributed to previous among-basin transfers of stock and local hatchery production in interior populations in the Russian River (Bjorkstedt et al. 2005). In San Francisco Bay streams, reduced population sizes and fragmentation of habitat has likely also led to loss of genetic diversity in these populations. For more detailed information on trends in CCC steelhead abundance, see: Busby et al. 1996, NMFS 1997, Good et al. 2005, Spence et al. 2008, Williams et al. 2011, and

Williams et al. 2016.

CCC steelhead have experienced serious declines in abundance and long-term population trends suggest a negative growth rate. This indicates the DPS may not be viable in the long term. DPS populations that historically provided enough steelhead immigrants to support dependent populations may no longer be able to do so, placing dependent populations at increased risk of extirpation. However, because CCC steelhead remain present in most streams throughout the

DPS, roughly approximating the known historical range, CCC steelhead likely possess a resilience that is likely to slow their decline relative to other salmonid DPSs or ESUs in worse condition. The 2005 status review concluded that steelhead in the CCC steelhead DPS remain

“likely to become endangered in the foreseeable future” (Good et al. 2005). On January 5, 2006, NMFS issued a final determination that the CCC steelhead DPS is a threatened species, as previously listed (71 FR 834).

A more recent viability assessment of CCC steelhead concluded that populations in watersheds that drain to San Francisco Bay are highly unlikely to be viable, and that the limited information available did not indicate that any other CCC steelhead populations could be demonstrated to be viable (Spence et al. 2008). The most recent status update concludes that steelhead in the CCC steelhead DPS remains “likely to become endangered in the foreseeable future” (Howe 2016), as new and additional information available since Williams et al. (2011) does not appear to suggest a change in extinction risk.

1 Population as defined by Bjorkstedt et al. 2005 and McElhaney et al. 2000 as, in brief summary, a group of fish of the same species that spawns in a particular locality at a particular season and does not interbreed substantially with fish from any other group. Such fish groups may include more than one stream. These authors use this definition as a starting point from which they define four types of populations (not all of which are mentioned here).

2.2.2 Status of CCC steelhead and CCC coho salmon critical habitat

In designating critical habitat, NMFS considers, among other things, the following requirements of the species: 1) space for individual and population growth, and for normal behavior; 2) food, water, air, light, minerals, or other nutritional or physiological requirements; 3) cover or shelter;

4) sites for breeding, reproduction, or rearing offspring; and, generally; and 5) habitats that are protected from disturbance or are representative of the historic geographical and ecological distributions of this species (50 CFR 424.12(b)). In addition to these factors, NMFS also focuses on Physical or Biological Features (PBF)2 and/or essential habitat types within the designated area that are essential to the conservation of the species and that may require special management considerations or protection (81 FR 7414).

PBFs for CCC steelhead critical habitat, and their associated essential features within freshwater include:

1. freshwater spawning sites with water quantity and quality conditions and substrate supporting spawning, incubation and larval development;

2. freshwater rearing sites with:

a. water quantity and floodplain connectivity to form and maintain physical habitat conditions and support juvenile growth and mobility;

b. water quality and forage supporting juvenile development; and

c. natural cover such as shade, submerged and overhanging large wood, log jams and beaver dams, aquatic vegetation, large rocks and boulders, side channels, and undercut banks;

3. freshwater migration corridors free of obstruction and excessive predation with water quantity and quality conditions and natural cover such as submerged and overhanging large wood, aquatic vegetation, large rocks and boulders, side channels, and undercut banks supporting juvenile and adult mobility and survival.

For CCC coho salmon critical habitat, the following essential habitat types were identified: 1) juvenile summer and winter rearing areas; 2) juvenile migration corridors; 3) areas for growth and development to adulthood; 4) adult migration corridors; and 5) spawning areas. Within these areas, essential features of coho salmon critical habitat include adequate: 1) substrate, 2) water quality, 3) water quantity, 4) water temperature, 5) water velocity, 6) cover/shelter, 7) food, 8) riparian vegetation, 9) space, and 10) safe passage conditions (64 FR 24029).

The condition of CCC coho salmon and CCC 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 habitat3: logging, agriculture, mining, urbanization, stream channelization and bank stabilization, dams, wetland

2 NMFS previously used the term “Primary Constituent Elements”, but has now shifted to using “Physical or

Biological Features. 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 primary constituent elements, physical or biological features, or both.”

3 Other factors, such as over fishing and artificial propagation have also contributed to the current population status of these species. All these human induced factors have exacerbated the adverse effects of natural environmental variability from such factors as drought and poor ocean productivity.

loss, and water withdrawals (including unscreened diversions for irrigation). Habitat 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/quantity, lost riparian vegetation, and increased sediment delivery into streams from upland erosion (Weitkamp et al. 1995; Busby et al. 1996; 64

FR 24049; 70 FR 37160; 70 FR 52488). Widespread diverting of rivers and streams, as well as the pumping of groundwater hydraulically connected to stream flow, has dramatically altered the natural hydrologic cycle in many of the streams within the CCC ESU and DPS, which can delay or preclude migration and dewater aquatic habitat.

2.2.3 Additional Threats to the CCC steelhead DPS and Critical Habitat of CCC steelhead and

CCC coho salmon

Another factor affecting the rangewide status of CCC coho salmon and steelhead, and aquatic habitat at large, is climate change. Global climate change presents an additional potential threat to salmonids and their critical habitats. Impacts from global climate change are already occurring in California. For example, average annual air temperatures, heat extremes, and sea level have all increased in California over the last century (Kadir et al. 2013). Snow melt from the Sierra Nevada has declined (Kadir et al. 2013). However, total annual precipitation amounts have shown no discernable change (Kadir et al. 2013). Listed salmonids may have already experienced some detrimental impacts from climate change. NMFS believes the impacts on listed salmonids to date are likely fairly minor because natural, and local, climate factors likely still drive most of the climatic conditions CCC steelhead experience, and many of these factors have much less influence on steelhead abundance and distribution than human disturbance across the landscape.

The threat to salmonids from global climate change will 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; critically dry years may increase (Lindley et al. 2007; Schneider 2007; Moser et al. 2012). Wildfires are expected to increase in frequency and magnitude (Westerling et al. 2011, Moser et al. 2012).

For Northern California, most models project heavier and warmer precipitation. Extreme wet and dry periods are projected, increasing the risk of both flooding and droughts (DWR 2013).

Estimates show that snowmelt contribution to runoff in the Sacramento/San Joaquin Delta may decrease by about 20 percent per decade over the next century (Cloern et al. 2011). Many of these changes are likely to further degrade CCC coho salmon and steelhead habitat by, for example, reducing streamflows during the summer and raising summer water temperatures.

Estuaries may also experience changes detrimental to salmonids. 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 et al. 2004; Osgood 2008; Turley

2008; Abdul-Aziz et al. 2011; Doney et al. 2012). The projections described above are for the mid to late 21st Century. In shorter time frames, climate conditions not caused by the human addition of carbon dioxide to the atmosphere are more likely to predominate (Cox and

Stephenson 2007; Santer et al. 2011).

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 Project encompasses the area within the existing county right-of-way, which is beyond the existing edge of pavement for SFDB, as well as select areas beyond the county right of way to encompass localized improvements (e.g., roadway realignment, culvert removal, and bridge and box culvert installation) on Schooner and East Schooner Creeks and an unnamed intermittent stream which flows into Drakes Bay. In addition, the Action Area extends

300 feet downstream of these areas to account for potential indirect effects to water quality as a result of construction activities. This area represents the location of temporary and permanent impacts. NMFS increased the action area to include Schooner Bay (Figure 1), an inlet of Drakes

Estero and downstream of Schooner and East Schooner Creeks, where sediment transport downstream is expected.

2.4 Environmental Baseline

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 consultation, and the impact of state or private actions which are contemporaneous with the consultation in process (50 CFR 402.02).

The project area is located on the Point Reyes Peninsula within PRNS. The peninsula is bordered by beaches, sea cliffs, and intertidal zones that gradually transition into the Pacific

Ocean, Drakes Bay, Drakes Estero, and Tomales Bay (NPS, 2009). The project area ranges in elevation from sea level to 1,200 feet. Rainfall averages approximately 12 inches per year at

Point Reyes, with the heaviest rainfall in December, January, February and March. Although there is little rain from mid-April through October, night and morning coastal fog condenses on the trees and vegetation which keeps the environment moist. Stream flow in Schooner and East

Schooner Creeks, and the unnamed intermittent stream which flows into Drakes Bay, varies seasonally. Generally the lower reaches of the tributaries rely on tidal influence during the summer months, and the winter storms can bring relatively high flows which contribute to the erosion along Sir Francis Drake Boulevard.

The NPS has historically focused on preservation and conservation rather than restoration of park lands. However, NPS has determined that without some action to improve aging infrastructure, and remove facilities that are no longer compatible with current land use, there is a real risk of catastrophic failure and degradation of NPS assets. NPS management recognizes the need to move beyond simple preservation by encouraging park units to restore natural systems and their associated processes, functions, and values (NPS 2004).

Within the PRNS, the Coastal Watershed Restoration Program was developed by the NPS to restore five coastal watersheds within the wilderness area. The objective of the program is to remove and restore physical impediments and correct abandoned roads associated with past land-use practices which are known to pose major ecological threats. The project includes a number of specific physical treatments within the five coastal watersheds, all draining into the Drakes

Estero system. Two of the projects, completed in 2008, replaced existing road crossing culverts with structures that allow for natural hydrologic process and fish passage for anadromous salmonids and other aquatic species on East Schooner Creek, within the Action Area (NPS

2009).

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

The proposed action includes replacement of two 7-foot diameter culverts at the Schooner Creek crossing with an approximately 57-foot long bridge, removal of an undersized culvert and replacement with a box culvert, and bank stabilization along approximately 710 of East Schooner

Creek, and tidal wetland restoration at historic wetlands on Drake’s Bay. Juvenile steelhead have been observed within East Schooner Creek in the reaches upstream of the project area where a higher gradient and flow, and cobble substrate are present. (Reichmuth 2015).

The existing twin culverts at Schooner Creek channelize and constrict water flow from both the freshwater entering Schooner Bay and the tidal flows that intersect with upstream habitats.

Essentially functioning as a dam during high tide and flow events, the culverts change the tidal dynamics, prevent natural mixing or circulation, and contribute to the stratification of the salinity levels. This stratification can lead to less than ideal conditions for steelhead as they transition from the fresh to saltwater environment.

The area of East Schooner Creek where the proposed bank stabilization, culvert removal and box culvert installation, would occur is characterized as a relatively low gradient area with fine substrate that is not considered to be suitable spawning habitat. The tidal wetland restoration area is currently separated from flow to Drake’s Bay; the project is designed to allow for passive inundation of tidal flow which will lead to wetland restoration over time.

2.4.2 Factors Affecting Species Environment within the Action Area

As described above, channelization caused by historic land use and road infrastructure is the major impact to salmonid habitat function within the reach of Schooner and East Schooner

Creeks flowing through the action area. NPS completed culvert replacement projects at two road crossings within the Action Area in 2008, which allowed for natural creek bed and step-pool structures. However, spawning gravel quality within the East Schooner Creek bank stabilization area is poor (high silt embeddedness) and pool frequency, depth and cover are sub-optimal.

Bank protection and use of culverts associated with SFDB along East Schooner Creek has caused channel incision and streambank failure, which has impaired riparian habitat and floodplain function (NPS 2006). East Schooner Creek is confined by proximity to SFDB, and thus suffers from loss of floodplain function. NMFS’ CCC steelhead recovery plan finds urbanization, water diversions, legacy timber harvest, and road-related sediment as the greatest stressors on instream habitat quality and quantity within the watershed (NMFS 2016). Recommended recovery actions focused on improving road construction and maintenance methods, increasing instream habitat complexity, and minimizing timber harvest and impacts from urban development. The high quality habitat within the watershed occurs where improved land management and stream restoration by the NPS have generally improved fluvial and geomorphic processes, or in areas that remain relatively untouched by historic land use.

In the long term, climate change may produce temperature, precipitation, and other changes that may adversely affect steelhead habitat in the action area. As described above, climate change will likely alter future rainfall patterns, durations and frequency across the region (Hayhoe et al.

2004). Stream systems lacking the ability to naturally evolve under increasingly variable precipitation patterns will likely suffer relatively greater climate change impacts, unless those critical processes are restored.

2.4.3 Previous Section 7 Consultations and Section 10 Permits in the Action Area

As described above, the Coast Watershed Restoration Project was implemented by the NPS in

2007 which included a completed Section 7 consultation in 2006.

Research and enhancement projects resulting from NMFS’ Section 10(a)(1)(A) research and enhancement permits and section 4(d) limits or…