Attachment5_Updated Regulatory Permit Application.pdf

UPDATED

REGULATORY PERMIT APPLICATION

MILITARY OCEAN TERMINAL CONCORD RESTORATION PROJECT

CONCORD, CONTRA COSTA COUNTY, CALIFORNIA

Prepared for: Prepared by:

U.S. Army Corps of Engineers San Francisco District 1455 Market Street San Francisco, California 94103

Volpe National Transportation Systems Center U.S. Department of Transportation 55 Broadway, Cambridge MA 02142

WRA, Inc.

2169-G East Francisco Boulevard San Rafael, CA 94901

Attn: Hope Kingma hope.kingma@wra-ca.com

WRA #30270

JUNE 2022

1.0 INTRODUCTION

This document provides supplemental information in support of applications for the United States Army Corps of Engineers (Corps) Clean Water Act (CWA) Section 404 Permit and a Regional Water Quality Control Board (RWQCB) Section 401 Water Quality Certification for the proposed Military Ocean Terminal Concord (MOTCO) Restoration Project located in northern Contra Costa County, California within the federally controlled Concord Naval Weapons Station (CNWS) lands (Figure 1, Part 4).

2.0 PROJECT DESCRIPTION

This section provides a description of information requested in:

• Corps Section 404 NWP – PCN Box 4a

• RWQCB Section 401 Water Quality Certification – Section 15

The USDOT proposes to decommission and remove the existing FAA infrastructure and restore the Project Area to near pre-existing conditions. This will include demolition and removal of all structures, concrete supports, enclosure fencing and restoration of tidally influenced wetlands providing a net increase in aquatic resource functions and services.

Work would commence with clearing all vegetation within the work areas to eliminate cover for the salt marsh harvest mouse (Reithrodontomys raviventris) (SMHM). Once vegetation has been removed, a construction crew using heavy equipment (e.g., an excavator, loader or similar) as well as other heavy equipment will be used to demolish any infrastructure, including removing fencing and associated footings, and all materials will then be hauled offsite for disposal. Once the structures are removed, any exposed gravel within the enclosure will be collected and similarly hauled offsite for disposal.

Once all structures are removed the site, the disturbed areas will be seeded with a native salt marsh seed mix to promote the re-establishment of salt marsh vegetation within the restored areas. In addition, emergent marsh vegetation is also expected to naturally revegetate from the remaining root stock (i.e., vegetation will be trimmed but not fully removed so that it may regrow the next season). The gravel access road will be abandoned in place and allowed to continue to become colonized by marsh vegetation (it is currently no more than a two-track access and is nearly fully vegetated).

Equipment used for the project will consist of heavy equipment (e.g., excavator or loader) used to demolish extant structures, dump trucks to haul cut vegetation or demolished materials away, pickup trucks to move crews and a variety of hand tools (e.g., weed whackers, mowers etc.) for supporting the operation.

2.1 Proposed Schedule

All Project activities will occur outside of the nesting season. Work will only occur from September 1 to January 31 and is anticipated to last one construction season. Work is expected to begin in 2022.

3.0 EXISTING CONDITIONS

3.1 Project Location

The Project Area is a 150-foot by 150-foot area located in the middle of an upper tidal marsh area that is enclosed by chain link fencing within MOTCO. The center of the Project Area supports two antennae structures and a small electrical housing unit. There is a remnant gravel road that provides access from the gate to the center of the Project Area; however, wetland vegetation is scattered along the gravel road.

The elevated gravel road that provides access to the Project Area has also been colonized by wetland and upland vegetation. Habitat conditions within the Project Area are generally intact with remnant and active structures in the center of the Project Area.

3.2 Waters of the United States

The project site contains features that are considered jurisdictional under Sections 404 and 401 of the Clean Water Act, including emergent marsh wetlands and salt pan wetlands.

On March 17, 2021, WRA, Inc. (WRA) conducted a delineation within the Project Area to identify wetlands and non-wetland waters potentially subject to jurisdiction by the U.S. Army Corps of Engineers (Corps) under Section 404 of the CWA. In addition, the delineation identified wetlands and other features potentially subject to jurisdiction of the California State Water Resources Control Board (SWRCB) and Regional Water Quality Control Board (RWQCB) as defined in the State Wetland Definition and Procedures for Discharges of Dredged or Fill Material to Waters of the State (State Wetland Policy, SWRCB, 2019).

WRA conducted the wetland delineation of the project site using criteria prescribed in the Corps’ 1987 Wetland Delineation Manual (Environmental Laboratory 1987) and the Corps’ Regional Supplement for the Arid West Region (Corps 2008). A draft wetland delineation map was submitted to the Corps along with a Request for a Jurisdictional Determination May 26, 2021. Part 5 provides the Delineation of Potential Waters of the U.S. and Waters of the State.

3.3 Biological Resources

3.3.1 Biological Communities

Developed areas include the gravel road, two FAA antennae structures and a small electrical housing unit.

Within the Project Area, emergent marsh wetlands are dominated by emergent marsh vegetation such as salt grass (Distichlis spicata), pickleweed (Salicornia pacifica) and buck's-horn plantain (Plantago coronopus), with coastal gumweed (Grindelia stricta) and coyote bush (Baccharis pilularis) growing along the perimeter of the fencing. Other wetland species present within the Project Area include brass buttons (Cotula coronopifolia), narrow-leaved cattail (Typha angustifolia), common reed (Phragmites australis), garden asparagus (Asparagus officinalis), perennial pepperweed (Lepidium latifolium), alkali weed (Cressa truxillensis) and water parsley (Oenanthe sarmentosa). Areas mapped as salt pans included patches of unvegetated open water areas that support less than 5 percent vegetative cover that are characterized by salt crusts and algal matting, indicating long-term inundation.

4.0 PROJECT IMPACTS

This section provides a description of information requested in:

• Corps Section 404 NWP – PCN Block 4c

• RWQCB Section 401 Water Quality Certification – Section 18

4.1 Temporary Impacts

The Project Area includes a 150-foot x 150-foot fenced enclosure which surrounds the FAA infrastructure plus a 10-foot buffer around the fenced enclosure. The Project will result in temporary impacts to 0.63 acres. There may be some re-distribution of surface soils to restore the level grade and fill in holes left by the removal of structures and support pilings.

The impacts to waters of the U.S. and State are illustrated in Figure 4 (Part 3). Table 1 summarizes the total impacts to jurisdictional features that would result from the proposed project.

TABLE 1. PROPOSED TEMPORARY IMPACTS TO JURISDICTIONAL WETLANDS AND WATERS

AQUATIC FEATURES TOTAL IMPACTS (ACRES)

Emergent Marsh Wetland 0.59

Salt Pan Wetland 0.04

Total 0.63 acres

4.2 Indirect Impacts

Project activities will result in ground disturbance which could result in increased sedimentation of the surrounding wetlands following grading and the onset of the rainy season; however, these impacts would be temporary, discrete, and localized, and would be minimized by measures described in Section 5, below.

4.3 Federally Listed Species

The following listed species may be affected by the proposed project:

• Salt marsh harvest mouse (SMHM: Reithrodontomys raviventris) – Endangered

The following listed species may be affected, but are not likely to be adversely affected by the proposed project:

• California Ridgway's rail (CRR: Rallus obsoletus obsoletus) – Endangered

The USDOT (applicant) is the federal nexus agency that will initiate Section 7 consultation with the USFWS pursuant to the Federal Endangered Species Act (FESA) for the proposed project. Part 6 of this application provides a Biological Assessment to facilitate Section 7 consultation. It is anticipated that the Corps will conduct informal consultation with USFWS pursuant to Section 7.

5.0 AVOIDANCE, AND MINIMIZATION MEASURES

• Corps Section 404 NWP – PCN Block 4d

• RWQCB Section 401 Water Quality Certification – Sections 16 and 19

The proposed project will include measures to avoid or minimize effects to listed species, sensitive habitats, and the surrounding environment. Any earthmoving activities would not be initiated until after preconstruction surveys determine that listed species are absent from the work area, and a biological monitor will be present during all ground-disturbing activities within salt marsh habitats to ensure appropriate vegetation removal and species avoidance measures are followed. Best management practices (BMPs) will be observed to minimize impacts, and specific Conservation Measures/Avoidance Measures listed in the BA will also be adhered to.

5.1 General Avoidance and Minimization Measures

The general conservation measures that will be implemented during the proposed project to avoid and minimize adverse effects on sensitive species and habitats are described. All permit conditions, legal requirements, and appropriate excavation and engineering practices shall be followed to avoid and minimize environmental impacts associated with the proposed project. BMPs will be implemented to avoid potential sedimentation issues during the proposed project.

• Areas of disturbance shall be limited to the Project Area, including access routes and staging areas.

• All equipment shall be maintained free of petroleum and/or synthetic fuel, lubricant, and hydraulic leaks.

• All staging, fueling, and maintenance of vehicles and equipment shall be confined to previously disturbed areas, or developed surfaces.

• The work site, areas adjacent to the work site, and access areas will be maintained in an orderly condition, free and clear from debris and discarded materials.

• Project-related vehicle traffic will be restricted to designated pathways to enter and exit the Project Area.

• Construction personnel will participate in a worker environmental awareness program. Under this program, construction personnel will be informed about the presence of listed species and habitats associated with the species and that unlawful take of the animal or destruction of its habitat is a violation of FESA. The program will also include species identification, life history, habitat requirements of these species, the importance of their associated habitats, and a list of measures being taken to reduce impacts on these species during construction. A sign-in sheet of the training will be retained on site. A fact sheet conveying this information will be available to workers on-site in an area that is readily available to workers.

• Erosion control measures around the project site following will be implemented in order to avoid or minimize potential for sedimentation of offsite habitats.

5.2 Avoidance and Minimization Measures for Salt Marsh Harvest Mouse

Given the number of records for salt marsh harvest mice (SMHM) in the vicinity of the project site, and the presence of pickleweed habitat in the project area, the Project’s construction activities could result in direct mortality and/or harassment of SMHM individuals. Moreover, SMHM could move into the work area during project construction. Finally, the proposed project will result in temporary impacts to marginal pickleweed habitat for this species; however, the pickleweed habitat will be restored and enhanced, providing a benefit to the species. Potential impacts will be minimized through implementation of the following avoidance measures.

• A qualified biological monitor will be present during all vegetation clearing and all ground disturbance in marsh habitats and in vegetated areas adjacent to marsh habitats. The monitor will have demonstrated experience in biological construction monitoring for SMHM and knowledge of the biology of the special-status species that may be found in the Project Area, including SMHM.

The monitor(s) will have the authority to halt construction, if necessary, to ensure that there is no take of federally listed species. The biological monitor(s) will be the contact person for any employee or contractor who might inadvertently kill or injure a potential special-status species or anyone who finds a dead, injured, or entrapped potential special-status species. If any mouse is injured or killed, all work will pause until the individual is identified to species by a qualified biologist.

• Vegetation clearing will occur prior to work with any heavy equipment. Vegetation clearing will be completed using only hand tools (e.g., string trimmers), and will occur as a two phased method when vegetation is taller than 12 inches. If vegetation is less than 12 inches, it may be cleared using Phase 2 methods only.

o Prior to any vegetation removal, the biological monitor will disturb vegetation using a broom or rake to allow SMHM to passively leave the area where vegetation will be removed and move into adjacent marsh areas (i.e., flush).

o Phase 1: Initial Cut - Once vegetation is surveyed by the biologist, any vegetation over 12 inches in height will be cut to a height of no less than 6 inches.

o Phase 2: Final Cut - For vegetation under 12 inches, or vegetation cut as prescribed in Phase 1, SMHM will be flushed from the work area and surveyed by the biologist. The vegetation will then be trimmed down to no taller than 2 inches. Once cut, all vegetation will be raked or gathered and removed from the work area to assure that any possible cover for SMHM is removed.

• Instead of a SMHM exclusion fence, a buffer of 10 feet will be cleared around the chain link fence to ensure that no mice are present in areas where they might be impacted by movement of equipment within the Project Area.

• Alternatively, an exclusion barrier and/or fencing may be installed to exclude individuals of this species from work areas. The design of the exclusion barrier and fencing will be approved by a qualified biologist and will be installed in the presence of a qualified biological monitor. The fence will be made of a material that does not allow SMHM to pass through, and the bottom will be buried to a depth of a minimum of 4 inches so that these species cannot crawl under the fence.

All support for the exclusion fencing will be placed on the inside of the project footprint.

5.3 Avoidance and Minimization Measures for California Ridgway’s Rail

The proposed project is not expected to result in direct impacts to California Ridgway’s rail. There are no tidal habitats within the Project Area that could provide habitat for CRR. However, suitable habitat does occur offsite within 700 feet of the Project Area. Potential disturbances to nesting CRR will be avoided through implementation of the following avoidance measures.

• All Project activities will occur outside of the nesting season. Work will only occur from September 1 to January 31.

• A biological monitor shall be onsite and if CRR are observed on the ground within the project area, the biologist shall halt any work within 100 feet of the individual until the animal leaves of its own volition.

6.0 HABITAT RESTORATION

• Corps Section 404 NWP – PCN Block 4d

• RWQCB Section 401 Water Quality Certification – Section 19

This Habitat Restoration and Monitoring Plan describes the proposed restoration goals and activities, restoration implementation and seeding plans, and maintenance and monitoring of those areas disturbed during the proposed project.

6.1 Wetland Restoration

The Habitat Restoration and Monitoring Plan will restore emergent marsh within the Project Area. All disturbed wetland areas within the work area will be restored to pre-existing conditions, or better, by removing the outdated infrastructure used by the FAA from the site, restore site conditions, and the disturbed areas will be seeded with a native salt marsh seed mix to promote the re-establishment of salt marsh vegetation within the restored areas. In addition, emergent marsh vegetation is also expected to naturally revegetate from the remaining root stock (i.e., vegetation will be trimmed but not fully removed so that it may regrow the next season).

The purpose of this seeding is to facilitate the re-establishment of vegetative cover and to restore habitat. Wetland areas will be hydroseeded with California native wetland seed mix, as available from a specialty native seed supply (Table 1 below). The native wetland seed mix is based on the native species that currently occur on the project site.

TABLE 2. PROPOSED WETLAND NATIVE HYDROSEED MIX

SCIENTIFIC NAME COMMON NAME SEEDING RATE

Salicornia pacifica; OBL Pacific pickleweed 20 lbs/acre

Frankenia salina; FACW Alkali heath 10 lbs/acre

Distichlis spicata; FAC Salt grass 10 lbs/acre

Bolboschoenus maritimus; OBL Salt-marsh bulrush 10 lbs/acre

Seed mixes will be applied at a minimum rate of 50 pounds per acre. Seeds may be adjusted based on seed availability. If the site is not accessible by hydroseed truck, broadcast seeding will be utilized to seed disturbed areas and hand-raked into disturbed areas.

7.0 MONITORING PLAN

• Corps Section 404 NWP – PCN Block 4d

• RWQCB Section 401 Water Quality Certification – Section 19

7.1 Overview

Success of the restoration effort will be evaluated by comparing the quantified measures of vegetative cover, density, and species-richness of the restored site to similar parameters within non-manipulated areas in the adjacent marsh. Baseline data, or data from nearby reference areas, may be used as the standard for comparison. Quantitative standards for success and the location(s) of the reference area(s) will be established during the first year of monitoring. Comparisons will be made until performance standards are met.

Mitigation for the proposed project has been designed in accordance with mitigation guidelines and USACE requirements under Section 404 of the Clean Water Act. Regulatory agencies typically require an annual mitigation monitoring report that includes data necessary to document compliance with success criteria as outlined in the permit conditions of approval. Monitoring data will include plant cover data, general condition of the restoration site, and site photographs. One site visit will be made in the summer of each monitoring year (July).

7.2 Monitoring Methods

Herbaceous ground cover in the restored wetland habitat areas within the Project Area will be monitored by visually estimating percent cover of hydrophytic cover in a total of 10 square meter quadrats placed randomly within the restored work area. Hydrophytic cover within the reference wetland areas will be monitored by visually estimating percent cover of observed species in a total of 10 square meter quadrats placed randomly within the reference marsh areas adjacent to the Project Area.

7.3 Monitoring Schedule

Monitoring will occur every year for five years following completion of restoration activities or until the Year 5 success criteria have been met. The purpose of the annual monitoring program is to ensure that plant community development is progressing as anticipated, to make certain that the site is in good physical condition, and, if necessary, implement the remedial action measures.

For reference, Year 0 (as-built) will be 2022 (or subsequent years if permitting or construction is delayed).

In Year 0, immediately following seeding and other restoration activities, WRA will prepare a report that documents "as-built" conditions, including seed mixes used in the wetland areas, and any deviation from the approved plan. WRA will establish permanent vegetation sampling locations and permanent photograph stations. Photographs taken from established photo stations will provide a visual baseline for comparison to photographs taken each subsequent year (Years 1-5). The monitoring sampling locations and photograph locations will be shown on the as-built map.

Years 1 through 5: During Years 1 through 5, WRA will monitor the habitat restoration areas in accordance with the methods presented above. Each year, a comprehensive annual report documenting the monitoring results will be prepared.

8.0 VEGETATION SUCCESS CRITERIA

The success of the habitat restoration will be monitored by a qualified biologist for a period not less than 5 years after site restoration. Vegetation monitoring will focus on the percent cover of seeded or other naturally occurring native, herbaceous plant species. Monitoring reports will provide the total percent cover of all plant species.

If the success criteria are not achieved at the end of 5 years, the Applicant is responsible for implementing remedial action measures, including additional seeding, weeding, invasive plant eradication and an extension of the monitoring period. The applicant or their legal assignee shall be responsible for reasonably funding the remedial action measures necessary for successful completion of the restoration effort.

TABLE 3. PERFORMANCE STANDARDS AND SUCCESS CRITERIA FOR WETLAND RESTORATION

CATEGORY SUCCESS CRITERIA YEAR 1 YEAR 2 YEAR 3 YEAR 4 YEAR 5

Restored Wetlands Species Cover

Restored wetlands will be colonized by at least 75% of the reference site absolute cover by wetland species (FACW or OBL) at the end of the 5-year monitoring period.

≥15% ≥30% ≥50% ≥65% ≥75%

Native Plant Cover Relative cover by native plant species in restored wetlands will be at least 75% of the relative cover by natives in the reference site at the end of the 5 years monitoring period.

≥15% ≥30% ≥50% ≥65% ≥75%

Invasive Species Less than 10% cover by invasive plant speciesa such as broadleaf pepperweed (Lepidium latifolium)

˂10% ˂10% ˂10% ˂10% ˂10%

9.0 MAINTENANCE DURING MONITORING PERIOD

Inspections during annual site visits will allow for the identification of any weed invasion problems (such as broadleaf pepperweed). Invasive weeds will be considered a problem in areas where they are the dominant cover type, threaten reestablishment of desirable species, or appear to be spreading off the restoration site. Weeds will be controlled using the "best available technology". Noxious weeds and other exotic plants will be removed from the restoration area so that the total cover does not exceed 10 percent aerial cover. Hand removal of these plants under direct supervision of a biologist will be the primary control mechanism for invasive species, but mechanical removal or herbicide application may also be used if deemed appropriate. Herbicides registered for use in aquatic ecosystems may be used to control invasive species. Such applications will be made in accordance with applicable local, state, and federal regulations. Herbicides will only be applied by a licensed applicator.

a Only those with a “High” or “Moderate” rating per the Cal-IPC Inventory List

10.0 MONITORING REPORTS

10.1 Annual Reports

Annual reports will be prepared that discuss monitoring methodology and results that includes all data necessary to document compliance with restoration goals. Monitoring reports will include the following elements:

(A) Introduction;

(B) Goals, objectives, and success criteria;

(C) Methods: a description of monitoring methods;

(D) Results: a discussion of vegetative conditions compared to reference site and success criteria;

(E) Summary and recommendations: a discussion of any recommendations as appropriate;

(F) Figures: figures will show the site location, restoration areas, sampling locations and photo-stations; and

(G) Photographs taken at photo-stations.

Full annual reports will be provided for each monitoring year, which will be submitted to the agencies and other interested agencies by December 31st of each monitoring year. If restored habitats within the restoration area demonstrate that they are successfully meeting established performance criteria early into the monitoring period, the Applicant may request early signoff from the agencies. A qualified biologist with experience in biological monitoring will supervise the report preparation. These reports will assess progress in meeting success criteria and identify any problems with sedimentation, erosion, and/or other general causes of unsuccessful revegetation of the impact areas. If necessary, recommendations or improvements will be made to ensure the success criteria will be met during the monitoring period.

10.2 Notification of Completion

Upon completion of five years of monitoring, or achievement of the Year 5 success criteria (whichever is sooner), a final report will be sent to the RWQCB, Corps, USFWS, and other interested agencies detailing the results of the final year of monitoring. If the restored areas have met the success criteria outlined above by the end of the monitoring period, then the proposed action in the final report will be for no further action. If the restored areas have not met the success criteria by the end of the monitoring period, then the final report may recommend additional corrective measures and/or extending the monitoring period.