VA Alameda Final 401 Permit.pdf

CLEAN WATER ACT SECTION 401 WATER QUALITY CERTIFICATION

AND ORDER

for the

VA Alameda Point Outpatient Clinic and Columbarium Project, City of Alameda, Alameda County

Sent via electronic mail: No hard copy to follow

Effective Date: July 27, 2021 Place ID: 867849

WDID #: 2 CW 439104

Corps File No: 2018-00036S

Permittee: U.S. Department of Veterans Affairs

San Francisco Health Care System 4150 Clement Street San Francisco CA 94121

Contact: Robert Bezek, Alameda Program Manager

(510) 934-5321

Robert.Bezek@va.gov Correspondence to: Robert Bezek

150 Muir Road (NorCal HCS), Martinez, CA 94553

Water Board Brian Wines Staff: 1515 Clay Street, Suite 1400 Oakland, CA 94612 Phone: (510) 622-5680 Email: Brian.Wines@waterboards.ca.gov

Water Quality Certification and Order CIWQS Place ID 867849 VA Alameda Point Outpatient Clinic and Columbarium Project WDID# 2 CW 439104 i

Table of Contents Certification and Order Coverage

1. Project

1.1 Site Description

1.2 Construction Details

2. Impacts to Waters of the State

2.1 Fill and Discharge

2.2 Beneficial Uses

3. Mitigation

4. California Environmental Quality Act (CEQA) Compliance

5. Conditions

5.1 Regulatory Compliance and Work Windows

5.2 General Construction

5.3 Pre-Construction Reporting and Other Requirements

5.4 Active Construction and Post-Construction Reporting Requirements

5.5 Mitigation Requirements

5.6 Post-Construction Stormwater Treatment

5.7 Administrative and General Compliance

5.8 Standard Conditions

5.9 Annual Fees

Water Quality Certification and Order CIWQS Place ID 867849

Certification and Order Coverage This Clean Water Act (CWA) section 401 Water Quality Certification (Certification) and Order (Order) is issued to the U.S. Department of Veterans Affairs (Permittee or VA).

Pursuant to CWA Section 404, the Permittee has applied to the U.S. Army Corps of Engineers (Corps), Regulatory Branch, for authorization to fill and discharge to waters of the U.S. pursuant to an Individual Permit (Corps File No. 2018-00036S).

The Permittee applied to the San Francisco Bay Regional Water Quality Control Board (Water Board) requesting Certification verifying that the VA Alameda Point Outpatient Clinic and Columbarium Project (Project) does not violate State water quality standards.

The Water Board received the Project application on July 13, 2020. An incomplete application letter was provided to the Permittee on August 10, 2020.

The following sections are derived from the application materials received on July 13, 2020, and supplemental information received on January 20, March 11, April 27, and June 7, 2021 (Application).

1. Project The Project purpose is to consolidate the services described below at one location for veterans. The VA has three divisions: the Veterans Health Administration, which provides medical and social support services to veterans; the Veterans Benefits Administration, which administers financial programs and other forms of assistance to veterans and their families; and the National Cemetery Administration, which provides veterans a final resting place and commemorates their service to the nation. These three administrations provide VA services to about 440,000 veterans in the San Francisco Bay Area. Currently, veterans receive administrative and medical services at multiple locations in the Oakland area, while cemetery facilities are located at even farther geographic locations in the region. As a result, veterans often have to travel to different locations to receive necessary services and care.

1.1 Site Description

The Project site is located on a portion of the former Naval Air Station Alameda property known as the U.S. Department of Veterans Affairs (VA) Transfer Parcel. The VA Transfer Parcel is approximately 624 acres and situated on a peninsula that extends into the South San Francisco Bay (Bay) in Alameda County (Figure 1 in Att. A) (Lat.

37.785167; Long. -122.318059). The Project will develop 112 acres of the VA Transfer Parcel to construct a Veterans Health Administration outpatient clinic, Veterans Benefits Administration outreach office, National Cemetery Administration columbarium national cemetery, and a conservation management office (Att. A, Fig. 2). In addition to the 112-acre development area, the existing stormwater management system will be upgraded.

1.2 Construction Details

The Project includes the following components:

Water Quality Certification and Order CIWQS Place ID 867849

• Developing the 20-acre Veterans Health Administration outpatient clinic, Veterans Benefits Administration outreach office, and associated parking.

• Constructing the 80-acre National Cemetery Administration columbarium national cemetery.

• Developing a conservation management office on 2.4 acres.

• Constructing the north access road and on-site utility infrastructure on 11 acres.

• Constructing three new storm drains reaching north from the VA Development

Area on easements that will be acquired from the City of Alameda and the Navy.

• Implementing onsite mitigation wetlands consisting of 7.3-acre of created tidal marsh, 3.3 acres of created new tidal marsh-upland transition zone, and 14.8 acres of enhanced, existing tidal marsh.

An 80-acre National Cemetery Administration columbaria-only, aboveground cemetery will be constructed in the VA Development Area over a period of about 120 years. The cemetery will be for cremated remains only and will include several wall-like structures with niches to house urns containing cremated remains.

The VA Transfer Parcel supports a colony of least tern, a species listed as endangered under the federal Endangered Species Act. The U.S. Fish and Wildlife Service (USFWS) issued a biological opinion in 2012, which lists specific measures to protect the existing least tern colony. The VA will construct a 2,500-square-foot conservation management office on about 2.4 acres in the VA Development Area to support USFWS’ conservation efforts onsite and in the region.

To construct the three new outfall structures, construction work areas will be temporarily dewatered in the Oakland Inner Harbor to allow access for trenching, shoreline slope stabilization, and installing the concrete outfall structures. Two temporary cofferdams will be installed at the outfall locations. Cofferdams will be constructed by driving sheet piles with a vibratory hammer to a depth of at least 10 feet into the substrate. Any existing rock riprap slope stabilization that may impede cofferdam installation will be temporarily removed. Cofferdam construction will occur at low tide. Once the cofferdams are installed and the work areas are dewatered, the outfall areas will be excavated to subgrade to allow for outfall construction and installation of rock riprap slope protection. Equipment will be staged on land and work will be conducted inside the cofferdam/containment. Upon completion of construction, the sheet pile cofferdams will be removed using a vibratory hammer. Any rock riprap removed for cofferdam installation will be returned to the shoreline.

Per- and polyfluoroalkyl substances (PFAS) contamination was recently discovered in the groundwater at Installation Restoration Site 14, Firefighter Training Area (IR 14).

The new storm drain lines will be installed to the immediate west and east of IR 14 (See the Sheet, IR – Storm Drain Exhibit May 24, 2016, in Att. A). Remediation of IR 14 is overseen by the U.S. Environmental Protection Agency (U.S. EPA), the California Department of Toxic Substances Control (DTSC), and the Water Board. The extent of IR 14 was originally based on the size of a vinyl chloride plume in groundwater. With the recent detection of PFAS, which are a common component of firefighting foams, in groundwater at IR 14, it is likely that contaminated groundwater extends beyond the

Water Quality Certification and Order CIWQS Place ID 867849 currently established boundary of IR 14. The Navy is developing a sampling and analysis program to better characterize the extent of PFAS contamination in soil and groundwater in the vicinity of IR 14. This sampling and analysis plan will be implemented by the Navy before the storm drain lines are constructed. The land owned by the City is subject to the Site Management Plan (SMP)1 prepared by the City in coordination with U.S. EPA, DTSC and the Water Board. The City’s SMP requires that groundwater containing PFAS be discharged to the sanitary sewer.

Before the Project constructs a new storm drain through the Navy property to the west of IR 14, an SMP must be developed for managing soil and groundwater that will be disturbed during construction of the storm drain line. Installation of the storm drain lines is currently scheduled for the second half of 2023.

Stormwater Treatment Stormwater infrastructure for the Project site has been designed to comply with the water quality treatment requirements in Provision C.3 of the Municipal Regional Stormwater National Pollutant Discharge Elimination System (NPDES) Permit (MRP) (Order No. R2-2015-0049, as amended; NPDES Permit No. CAS612008). Runoff from impervious surfaces at the Project site will be treated in bioretention cells and drop inlet trash capture devices. Bioretention cells are sized to provide a treatment area surface area that is at least equal to four percent of the effective impervious area of each drainage management area (See the Sheets titled Stormwater Management Plan C101, Stormwater Management Plan C102, and RWQCB Stormwater Management Concept Plan in Att. A). The bioretention areas will be lined to prevent groundwater from affecting the bioretention cells. In some locations within the cemetery portion of the Project site, pumps will be required to remove water from low lying bioretention cells.

This Certification requires the Permittee to implement the Storm Water Treatment System Operation and Maintenance Plan for VA Multi-Specialty Outpatient Clinic Columbarium, and Conservation Management Office Alameda Point, Alameda, California (Corps, Sacramento District, December 17, 2020).

2. Impacts to Waters of the State The Water Board independently reviewed the Project record to analyze impacts to water quality and the environment and designated beneficial uses within the Project’s watershed.

2.1 Fill and Discharge

The Project will result in direct impacts from the placement of fill, and indirect impacts from the discharge of urban runoff to waters of the State for the life of the Project.

Constructing the Project in the 112-acre VA Development Area will permanently fill a total of 10.9 acres of wetlands and temporarily impact approximately 13.76 acres of

1 Final Site Management Plan, Alameda Point, Alameda, California (Terraphase Engineering, Inc., Dec. 3, 2020).

Water Quality Certification and Order CIWQS Place ID 867849 wetlands, salt marsh, and other waters over the proposed 120-year decadal-phased construction period (Att. A, Fig. 4). Construction of Phase I will permanently impact 3.57 acres of wetlands and temporarily impact 13.76 acres of open water, salt marsh, and wetlands. Permanent impacts to waters of the State will result from construction of the VA outpatient clinic and Veterans benefits office, national cemetery, conservation management office, north access road, and stormwater management system improvements. Temporary impacts to waters of the State will be associated with in-water work at the two new storm drain outfalls to the Oakland Inner Harbor and the construction of the tidal marsh creation and enhancement at the onsite mitigation wetland. Project phases two through 12 will permanently impact a total of 7.32 acres of wetlands.

The impacted wetlands consist primarily of seasonal wetlands dominated by nonnative species, such as tall fescue (Festuca arundinacea), velvet grass (Holcus lanatus), Bermuda grass (Cynodon dactylon), Mediterranean barley (Hordeum marinum), curly dock (Rumex crispus), annual bluegrass (Poa annua), Italian ryegrass (Lolium multiflorum), and loosestrife (Lythrum hyssopifolia). Native species present include common nut-sedge (Cyperus eragrostis), Baltic rush (Juncus balticus), creeping spikerush (Eleocharis macrostachya), and toad rush (Juncus bufonius). Nontidal salt marsh composes a small proportion of the impacted wetlands and is dominated by native salt marsh species, including pickleweed (Salicornia pacifica) and saltgrass (Distichlis spicata). Characteristic nonnative species include cranesbill (Geranium dissectum), red-stemmed filaree (Erodium cicutarium), Mediterranean barley, bird’s-foot trefoil (Lotus corniculatus), red sandspurry (Spergularia rubra), and bull thistle (Cirsium vulgare)

Impacts to waters of the State are summarized for each phase of development in Tables 1A and 1B. The first phase of construction, anticipated to begin in 2021 and end in 2026, will include raising the ground level at the Project site, geotechnical mitigation, construction of the onsite mitigation wetlands, construction of the stormwater system, construction of stormwater outfalls, construction of the Veterans Health Administration outpatient clinic, construction of the Veterans Benefits Administration outreach office, construction of the USFWS conservation management office, and construction of the first phase of the National Cemetery Administration columbarium national cemetery.

The 11 future phases of construction will expand the cemetery as capacity is needed.

Future phases are estimated to occur every 10 years over the next 120-plus years.

Water Quality Certification and Order CIWQS Place ID 867849

Table 1A. Permanent and Temporary Impacts to Waters of the State During Implementation of Phase 1 of the Project.

Feature ID Feature Class Impact Type Project Component

Impact Acreage

B1 Open Water Permanent Storm Drain Riprap 0.0017 B3 Open Water Permanent Tidal Inlet 0.0020

W2 Seasonal Wetland Permanent VA Development Area 0.4476

W23 Seasonal Wetland Permanent VA Development Area 0.4249

W25 Seasonal Wetland Permanent VA Development Area 2.1251

W26 Seasonal Wetland Permanent VA Development Area 0.2608

W27 Seasonal Wetland Permanent VA Development Area 0.1117

W28 Seasonal Wetland Permanent VA Development Area 0.2003

Total permanent impacts Phase 1 3.5741 B1 Open Water Temporary Storm Drain Temporary Construction Buffer 0.0247 B2 Open Water Temporary Storm Drain Temporary Construction Buffer 0.0104 B3 Open Water Temporary Tidal Inlet 15 ft Buffer 0.0313 S16 Saltmarsh Temporary Wetland Enhancement Area 3.9276 S17 Saltmarsh Temporary Wetland Enhancement Area 3.4854 S18 Saltmarsh Temporary Storm Drain Temporary Construction Buffer 0.0153

U3 Unvegetated Water Temporary Wetland Enhancement Area 5.8837

W16 Seasonal Wetland Temporary Wetland Enhancement Area 0.3865

Total temporary impacts Phase 1 13.7649

Feature IDs are labeled in Att. A, Fig. 4.

Water Quality Certification and Order CIWQS Place ID 867849

Table 1B. Permanent Impacts to Waters of the State During Implementation of Phases 2 Through 12 of the Project.

Phase Feature

ID Feature Class Project Component Impact

Acreage 2 W2 Seasonal Wetland VA Development Area 1.3153 3 W2 Seasonal Wetland VA Development Area 0.7695 4 W23 Seasonal Wetland VA Development Area 0.3082 4 W25 Seasonal Wetland VA Development Area 0.0901

Sub-total permanent impacts Phase 4 0.3983 5 W23 Seasonal Wetland VA Development Area 0.4172 6 S2 Saltmarsh VA Development Area 0.0485 6 W24 Seasonal Wetland VA Development Area 0.0167 6 W3 Seasonal Wetland VA Development Area 0.6650

Sub-total permanent impacts Phase 6 0.7303 7 S2 Saltmarsh VA Development Area 0.1611 7 W3 Seasonal Wetland VA Development Area 0.3995

Sub-total permanent impacts Phase 7 0.5606 8 W1 Seasonal Wetland VA Development Area 0.8471 9 W3 Seasonal Wetland VA Development Area 0.9855 11 W23 Seasonal Wetland VA Development Area 0.2407 11 W24 Seasonal Wetland VA Development Area 0.6620

Sub-total permanent impacts Phase 11 0.9028 12 W1 Seasonal Wetland VA Development Area 0.3977

Total permanent impacts future phases 7.3243

Feature IDs are labeled in Att. A, Fig. 4.

2.2 Beneficial Uses

The San Francisco Bay Basin Water Quality Control Plan (Basin Plan) defines the beneficial uses of waters of the State. The Project will impact waters of the State consisting of the Oakland Inner Harbor, San Francisco Bay Lower, and seasonal wetlands. The Oakland Inner Harbor has existing beneficial uses of estuarine habitat, wildlife habitat, water contact recreation, water non-contact recreation, and navigation.

San Francisco Bay Lower has existing beneficial uses of industrial supply, commercial and sport fishing, shellfish harvesting, estuarine habitat, fish migration, preservation of rare and endangered species, fish spawning, wildlife habitat, water contact recreation, water non-contact recreation, and navigation. Seasonal wetlands at the Project site are likely to support the beneficial uses of the preservation of rare and endangered species and wildlife habitat.

3. Mitigation Permanent impacts to waters of the State from construction of Phase 1 have been compensated through the purchase of 3.6 acres of mitigation credits from the San Francisco Wetland Mitigation Bank on March 17, 2017. The Water Board has been provided with documentation that confirms the purchase of the mitigation credits.

Water Quality Certification and Order CIWQS Place ID 867849

To mitigate impacts to waters of the State in Phases 2 through 12, the VA will create 7.3 acres of new jurisdictional tidal marsh at the southern end of Alameda Point, bordered by at least 3.3 acres of new tidal marsh-upland transition zone (transition zone) around the created marsh to increase resilience of the created marsh to sea level rise. This area is referred to as the tidal marsh creation area. In addition, the VA will enhance the function of existing tidal marsh, salina, and transition zone habitat located immediately east of the tidal marsh creation area through a combination of invasive plant control and native plant installation. This 14.8-acre area is referred to as the tidal marsh enhancement area (Att. A, Fig. 5).

The construction, monitoring, and maintenance of the on-site mitigation wetlands is described in the Alameda Point Veterans Affairs Project Final Wetland Mitigation and Monitoring Plan (MMP) (H. T. Harvey & Associates, June 2, 2021). Construction in the mitigation area will include excavation of the existing ground surface to elevations suitable for the establishment of a pickleweed (Salicornia spp.) dominated tidal marsh.

Pilot channels will be excavated into the tidal marsh mitigation area to encourage development of a dendritic slough channel network that emulates the structure and function of those found in naturally occurring, mature tidal marsh systems of similar size. The grading design plan view for the tidal marsh creation area is provided in Att. A, Fig. 7. Att. A, Fig. 8 presents typical cross sections showing the created tidal marsh, tidal channels, and tidal inlet design. The revegetation design plan view and cross section for the tidal marsh creation area are provided in Att. A, Figs. 9 and 10.

To provide adequate tidal exchange between the on-site mitigation area and the Bay, an inlet channel will be constructed at the south end of the mitigation site (Att. A, Fig. 8).

Inlet channel construction will remove a portion of the existing rock seawall. In addition, a training dike will be constructed behind the mouth of the inlet channel to convey waters into the pilot channel system. To remove a portion of the seawall and construct the inlet channel, a temporary construction work area will be isolated from the Bay.

Vegetation in the tidal marsh creation area currently consists primarily of nonnative, invasive species including iceplant interspersed with ripgut brome (Bromus diandrus), stinkwort (Dittrichia graveolens), Italian thistle (Carduus pycnocephalus), and black mustard (Brassica nigra) (Att. A, Fig. 6). Vegetation in the tidal marsh enhancement area consists of perennial pickleweed interspersed with fleshy jaumea (Jaumea carnosa), saltgrass, and marsh rosemary (Limonium californicum). A large population of nonnative, invasive Algerian sea lavender is established at the southern end of the marsh near the tidal channel. Algerian sea lavender is a “highest priority” plant species for control in tidal salt marsh habitats in South San Francisco Bay, because it invades restored and disturbed marshes, spreads by buoyant seed through tidal waters, and displaces native plants. Eradication of this plant during Project implementation is necessary to enhance the existing tidal marsh and establish the adjacent created tidal marsh habitat without invasion of Algerian sea lavender. Vegetation in the transition zone is dominated by invasive iceplant interspersed with ripgut brome and saltgrass. Non-native ruderal vegetation will be removed by clearing and grubbing the areas shown in Figure 11 in

Water Quality Certification and Order CIWQS Place ID 867849

Att. A by scraping the vegetative matter and upper three to six inches of topsoil with seedbank prior to grading for wetland creation and enhancement.

The created tidal marsh plain will be vegetated with a diversity of native tidal marsh plants established across an elevational gradient from about 1 foot above mean sea level (MSL) to above mean higher high water (MHHW) (Att. A, Figs. 9 and 10). Low-marsh vegetation, primarily Pacific cordgrass, will grow along tidal channels from approximately 1 foot above MSL to mean high water (MHW). The midmarsh plain (from MHW to MHHW) will be dominated by perennial pickleweed interspersed with patches of annual pickleweed (Salicornia depressa), fleshy jaumea, and seaside arrow grass (Triglochin maritima). The high-marsh plain (at MHHW) will be vegetated primarily with perennial pickleweed with patches of fleshy jaumea, saltgrass, alkali heath (Frankenia salina), and other native tidal marsh plants that grow near the high end of the elevation range of San Francisco Bay tidal marshes. Detailed planting palettes for the components of the mitigation site are presented in MMP Tables 6 through 10.

The mitigation wetlands and transition areas will be monitored and maintained until the Year 5 success criteria in Tables 2 and 3 are attained.

Table 2. Performance and Success Criteria for the Tidal Marsh Creation Area

Annual Performance/Final Success Criterion

Year 1

Year 2

Year 3

Year 4

Year 5

Tidal Marsh Wetland Delineation - - ≥7.3 ac - -

Hydrology/Acreage ≥7.3 ac below HTL

≥7.3 ac below

HTL

≥7.3 ac below HTL

≥7.3 ac below HTL

≥7.3 ac below HTL

Percent Cover Native Species - >Year 1 >Year 2 >Year 3 ≥60% Native Plant Diversity >baseline >baseline >baseline >baseline >baseline

Invasive Plant Cover ≤5% ≤5% ≤5% ≤5% ≤5%

Vegetation Height <2 feet <2 feet <2 feet <2 feet <2 feet

Topographic Change and Tidal Inlet Stability

Qualitative expert opinion

Qualitative expert opinion

Qualitative expert opinion

Qualitative expert opinion

Qualitative expert opinion

Transition Zone

Percent Cover Native and Nonnative Species

- >Year 1 >Year 2 >Year 3 ≥60%

Native Plant Diversity >baseline >baseline >baseline >baseline >baseline

Invasive Plant Cover ≤5% ≤5% ≤5% ≤5% ≤5%

Vegetation Height <2 feet <2 feet <2 feet <2 feet <2 feet

Water Quality Certification and Order CIWQS Place ID 867849

Table 3. Performance and Success Criteria for the Tidal Marsh Enhancement Area

Annual Performance/Final Success Criterion Year 1 Year 2 Year 3 Year 4 Year 5

Tidal Marsh Native Plant Diversity >baseline >baseline >baseline >baseline >baseline

Invasive Plant Cover ≤5% ≤5% ≤5% ≤5% ≤5%

Vegetation Height ≤2 feet ≤2 feet ≤2 feet ≤2 feet ≤2 feet

Transition Zone Percent Cover Native and Nonnative Species - >Year 1 >Year 2 >Year 3 ≥60%

Native Plant Diversity - >baseline >baseline >baseline >baseline

Invasive Plant Cover ≤5% ≤5% ≤5% ≤5% ≤5%

Vegetation Height <2 feet <2 feet <2 feet <2 feet <2 feet

Long-term management of the of on-site mitigation wetlands will be provided by implementing the Long-Term Management Plan in MMP Section 7.

4. California EcoAtlas Regional, state, and national studies have determined that tracking of mitigation and restoration projects must be improved to better assess the performance of these projects, following monitoring periods that last several years. To effectively carry out the State’s Wetlands Conservation Policy of no net loss to wetlands, the State needs to closely track both losses and successes of mitigation and restoration projects affecting wetlands and other waters of the State. The Water Board must also track project performance in Bay Area creeks subject to routine repair and maintenance activities, such as recurring instabilities. Therefore, we adopted the digital interactive mapping tool called EcoAtlas.2 EcoAtlas is a web-based tool that integrates maps, project plans, site conditions, restoration efforts, and other elements on a project-by-project basis based on data inputs. Accordingly, we require the Permittee to upload their Project information to EcoAtlas with the Project Tracker tool at https://ptrack.ecoatlas.org. The California Wetlands Monitoring Workgroup developed EcoAtlas and maintains detailed instructions for Project Tracker on its website at https://ptrack.ecoatlas.org/instructions.

5. California Environmental Quality Act (CEQA) Compliance In compliance with the requirements of the National Environmental Policy Act (NEPA), the VA prepared an Environmental Assessment, VA Alameda Point Multi-Specialty Outpatient Clinic and Columbarium (HDR, November 2013) and Final Supplemental

2 Source: California Wetlands Monitoring Workgroup (CWMW), 2019. EcoAtlas. Accessed May 14, 2019. https://www.ecoatlas.org. The California Wetland Monitoring Workgroup (CWMW) provides technical oversight on the development of content and functionality of EcoAtlas. As a member of CWMW, San Francisco Estuary Institute provides day-to-day support and management of EcoAtlas, and can be contacted by email at ptrackadmin@sfei.org.

https://ptrack.ecoatlas.org/ https://ptrack.ecoatlas.org/instructions https://gcc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ecoatlas.org%2F&data=02%7C01%7Csusan.glendening%40waterboards.ca.gov%7Cbaa063561b3f4c44307b08d719478765%7Cfe186a257d4941e6994105d2281d36c1%7C0%7C0%7C637005667327983293&sdata=qH7%2BpABGBKY9C5dTw3qbMjrW%2BEPtnAZWpYD4PKTMAcA%3D&reserved=0 mailto:ptrackadmin@sfei.org

Water Quality Certification and Order CIWQS Place ID 867849

Environmental Assessment, VA Alameda Point Multi-Specialty Outpatient Clinic and Columbarium (HDR, May, 2021). On April 15, 2021, the VA signed a Finding of No Significant Impact (FONSI) for the Project.

Per CEQA Guidelines Section 15221:

When a project will require compliance with both CEQA and National Environmental Policy Act (NEPA), state or local agencies should use the EIR or Finding of No Significant Impact (FONSI) rather than preparing an Environmental Impact Report (EIR) or Negative Declaration if the following two conditions occur: An EIR or FONSI will be prepared before an EIR or Negative Declaration would otherwise be completed for the project; and (2) The Environmental Impact Statement or FONSI complies with the provisions of these Guidelines.

The Water Board, as a responsible agency under CEQA, has reviewed the Project’s mitigation measures in the NEPA documents prepared by the VA and has determined that the Project’s impacts to waters of the State have been appropriately evaluated and that compliance with the NEPA mitigation measures and the mitigation activities described in the body of this Certification and required by the Certification’s conditions will mitigate the Project’s impacts to waters of the State to a less than significant level.

6. Conditions I, Michael Montgomery, Executive Officer, do hereby issue this Order certifying that any discharge from the proposed Project will comply with the applicable provisions of sections 301 (Effluent Limitations), 302 (Water Quality Related Effluent Limitations), 303 (Water Quality Standards and Implementation Plans), 306 (National Standards of Performance), and 307 (Toxic and Pretreatment Effluent Standards) of the Clean Water Act, and with other applicable requirements of State law. This discharge is also regulated under State Water Resources Control Board Order No. 2003-0017-DWQ, “General Waste Discharge Requirements for Dredge and Fill Discharges That Have Received State Water Quality Certification,” which requires compliance with all conditions of this Order, including the following:

6.1 Regulatory Compliance and Work Windows

1. Design Conformance. Project components associated with constructing the new outfalls and the onsite mitigation wetlands shall be constructed in conformance with the Project description provided in the Application, the body of this Certification, and the design sheets in Att. A. Any changes to designs provided in the Application must be submitted to the Water Board and receive Executive Officer approval before the changes may be implemented;

2. Corps Compliance. The Permittee shall adhere to the conditions of the Individual Permit issued by the Corps (Corps File No. 2018-00036S);

Water Quality Certification and Order CIWQS Place ID 867849

3. Work Window. Construction in waters of the State along the shoreline is restricted to the June 1 to November 30 work window set by the National Marine Fisheries Service (NMFS) to protect special status species in San Francisco Bay;

4. Worker Educational Awareness Program. Prior to Project commencement, a Worker Environmental Awareness Program (WEAP) shall be implemented to educate all construction personnel of the area's environmental concerns and conditions, including special-status and listed species, site contamination prevention, and other relevant environmental concerns and appropriate work practices, including spill prevention, emergency response measures, protection of special-status resources, and proper implementation of best management practices (BMPs), to all construction and maintenance personnel. Any new workers who arrive after construction has started shall be trained under the WEAP within two days of starting work at the Project site;

5. Precipitation and Construction Planning. Precipitation forecasts shall be considered when planning construction activities. The Permittee shall monitor the 72-hour forecast from the National Weather Service at https://www.weather.gov. When there is a forecast of more than 40% chance of rain, or at the onset of unanticipated precipitation, the Permittee shall remove all equipment from the shoreline area and shall implement erosion and sediment control measures (see Condition 6), and all Project activities shall cease, and can resume once precipitation has stopped for a 12-hour period, and there is not a 40% chance of rain in the next 72 hours;

6.2 General Construction

6. Discharge Prohibition. No unauthorized construction-related materials or wastes (e.g., debris, soil, silt, excessive bark, rubbish, creosote-treated wood, raw cement/concrete or washings thereof, asphalt, paint or other coating material, oil or other petroleum products, or any other substances which could be hazardous to aquatic life) shall be allowed to enter into or be placed where they may be washed by rainfall or runoff into waters of the State. To the maximum extent practicable, work along the shoreline shall be conducted at low tide. When construction is completed, any excess material shall be removed from the work area and any areas adjacent to the work area where such material may be discharged to waters of the State. The Applicant shall obtain coverage under and comply with the Statewide NPDES Construction Stormwater General Permit (State Water Resources Control Board Order No. 2009-0009-DWQ, as amended). This includes the following requirements;

a. Prior to the start of the rainy season, the Applicant shall ensure that disturbed areas of waters of the State and disturbed areas that drain to waters of the State are protected with correctly-installed and -maintained erosion control measures (e.g., jute, straw, coconut fiber erosion control https://www.weather.gov/

Water Quality Certification and Order CIWQS Place ID 867849 fabric, coir logs, etc.), and/or revegetated with propagules (seeds, cuttings, divisions) of locally collected native plants. Erosion control textiles that include plastic monofilament netting are prohibited from use at the Project Site or at the Mitigation Site;

b. Where areas of bare soil are exposed during the rainy season, appropriate erosion and sediment control measures shall be used where sediment and/or earthen fill threaten to enter waters of the State, consistent with the requirements. Sediment control structures shall be monitored for effectiveness and shall be repaired or replaced as needed. Buildup of soil behind silt fences shall be removed promptly and any breaches or undermined areas repaired at once;

7. Permission to Work on Lands Owned by the Navy and City of Alameda. The western new storm drain line will cross land that is owned by the Navy and the eastern new storm drain line will cross land that is owned by the City. Before commencing work on land owned by the Navy or City, the Permittee shall provide the Water Board’s Executive Officer with written documentation that the landowner has granted the Permittee permission to work on their property;

8. Management of Contaminated Soils and Groundwater Encountered During Excavation for New Storm Drain Lines. The new storm drain lines will be installed to the west and east of IR Site 14, which is contaminated with vinyl chloride and PFAS. The City has developed a Site Management Plan (SMP)3 in coordination with U.S. EPA, DTSC, and the Water Board. Prior to excavating soil and/or pumping groundwater to dewater the excavation on City property, the Permittee shall submit a workplan for management of soil and groundwater to the Water Board’s Executive Officer for review and approval. The workplan shall be consistent with the SMP and describe how soil and groundwater will be managed to prevent discharging contaminants to waters of the State at concentrations that may impair the beneficial uses of the Oakland Inner Harbor. The Navy is in the process of developing a SMP for land owned by the Navy in coordination with U.S. EPA, DTSC and the Water Board.

Prior to excavating soil and/or pumping groundwater to dewater the excavation on Navy property, the Permittee shall submit a workplan for management of soil and groundwater to the Water Board’s Executive Officer for review and approval. The workplan shall be consistent with the Navy’s SMP and describe how soil and groundwater will be managed to prevent discharging contaminants to waters of the State at concentrations that may impair the beneficial uses of the Oakland Inner Harbor;

9. Construction Dewatering. No later than 30 days prior to dewatering either of the new outfall construction sites or the area of the Bay adjacent to the tidal inlet for the mitigation wetlands, the Permittee shall submit a

3 Final Site Management Plan, Alameda Point, Alameda, California (Terraphase Engineering, Inc., Dec. 3, 2020).

Water Quality Certification and Order CIWQS Place ID 867849 final dewatering plan for each dewatered work site to the Water Board.

The dewatering plan must be consistent with the description of dewatering in the body of this Certification and include any dewatering guidance provided in Biological Opinions provided by USFWS and/or NMFS. The Project work areas in the Oakland Inner Harbor or Bay shall not be dewatered until the Permittee has received written approval of the final dewatering plan from the Water Board’s Executive Officer;

10. Equipment Cleaning and Maintenance. Prior to use, all equipment must be cleaned to remove external oil, grease, dirt, or mud. Wash sites must be located in upland locations so that wash water does not flow into waters of the State. Project personnel shall remove mud, snails, algae, and other debris from nets, traps, boots, vehicle tires, and all other surfaces;

11. Equipment Maintenance Prohibition. No fueling, cleaning, or maintenance of vehicles or equipment shall take place within waters of the State, or within any areas where an accidental discharge to waters of the State may occur; and construction materials and heavy equipment must be stored outside of the active flow of the creek or other waters of the State;

12. Impacts to Beneficial Uses. All work performed within waters of the State shall be completed in a manner that minimizes impacts to beneficial uses and habitat; measures shall be employed to minimize disturbances along waters of the State that will adversely impact the water quality of waters of the State. Disturbance or removal of vegetation shall not exceed the minimum necessary to complete the Project;

6.3 Pre-Construction Reporting and Other Requirements

13. EcoAtlas. The Permittee shall input Project information to EcoAtlas within

14 days from the date of this Order. The Project information shall be added to the Project Tracker tool in EcoAtlas online at https://ptrack.ecoatlas.org. Instructions for adding information to EcoAtlas are available at https://ptrack.ecoatlas.org/instructions, or by contacting the San Francisco Estuary Institute by email at ptrackadmin@sfei.org, or the Water Board case manager listed on the cover page of this Order. The Executive Officer may grant an extension to the 14-day deadline if the Permittee submits a request in writing to the Water Board case manager listed on the cover page of this Order. The extension request may be submitted via electronic mail. If any changes to the project occur pursuant to Conditions 19, 20, 21, 22, or 23 the Permittee shall revise EcoAtlas information for the Project, accordingly. In cases when EcoAtlas must be revised, the Permittee shall meet the same schedule and notification requirements required for the initial EcoAtlas information;

https://ptrack.ecoatlas.org/ https://ptrack.ecoatlas.org/instructions mailto:ptrackadmin@sfei.org

Water Quality Certification and Order CIWQS Place ID 867849

14. Commencement of Construction. The Permittee shall submit a Commencement of Construction Report at least seven days prior to start of initial ground disturbance activities and notify the Water Board at least 48 hours prior to initiating in-water work. Notification may be via telephone, email, delivered written notice, or other verifiable means;

15. Photo-Documentation Points. Prior to the start of construction of the new outfalls and the onsite wetland mitigation area, the Permittee shall establish a minimum of two photo-documentation points at each outfall construction site and 10 photo-documentation points at the mitigation wetlands, for a total of 14 photo-documentation points. At the outfall construction sites, the photo-documentation points shall be selected to document the condition of shoreline armoring before and after construction of the outfalls. At the onsite mitigation wetland, the photo-documentation points shall include representative views of the inlet through the shoreline armoring, the pilot channels in the created wetland, vegetation in the created wetland, vegetation in the transition zone, and vegetation in the enhanced wetland. The Permittee shall prepare site maps with the photo-documentation points clearly marked. Pre-construction and post-construction photographs from each of the four outfall photo-documentation points and the maps shall be submitted, along with the as-built reports for the outfalls (See Condition 16). Post-construction photographs from each of the 10 photo-documentation points at the onsite mitigation wetlands and the maps shall be submitted, along with the as-built report for the onsite mitigation wetlands (See Condition 16);

6.4 Active Construction and Post-Construction Reporting Requirements

16. As-Built Reports Not later than 60 days after completing construction of the new outfalls and the onsite wetland mitigation area, the Permittee shall submit an as-built report to the Water Board for each of these Project components. The reports shall include a description of the areas of actual disturbance during Project construction and the photographs and maps specified in Condition 15. The as-built report shall include the 100 percent construction plans, marked with the contractor’s field notes, that clearly depict any deviations from the design sheets that were made during construction. The as-built report shall provide a written explanation of the need for any deviations from the approved Project plans;

17. Project Construction Completion Report. Not later than 60 days after completing Project construction activities for the stormwater outfalls, the onsite mitigation wetlands, and all Phase 1 Stormwater Facilities (See Condition 26), the Permittee shall submit, acceptable to the Executive Officer, a Notice of Project Construction Completion that references CIWQS Place ID 867849. The Notice shall include the as-built reports (see Condition 16), the date of the first Project related disturbance of

Water Quality Certification and Order CIWQS Place ID 867849 waters of the State occurred, and the date construction of the Project components listed in this condition was completed. The Notice shall be sent via email to RB2-401Reports@waterboards.ca.gov, or by mail to the attention of 401 Certification Reports (see address on the letterhead);

18. Annual Project Status. The Permittee shall submit an Annual Project Status Report each year by January 31 commencing the calendar year after issuance of this Certification. The Report shall reference CIWQS Place ID 867849 and state whether Project construction activities have been initiated or delayed. The Annual Project Status Report shall continue until a Notice of Project Construction Completion is received (see Condition 17), upon completion of all work with impacts to waters of the State, including the construction of all Stormwater Facilities at the Project site;

6.5 Mitigation Requirements

19. Implementation and Documentation of Mitigation. The Permittee shall implement the mitigation measures described in the Alameda Point Veterans Affairs Project Final Wetland Mitigation and Monitoring Plan (MMP) (H. T. Harvey & Associates, June 2, 2021). Construction of the onsite mitigation wetland shall commence no later than one year after the first impacts to waters of the State at the Project site. The onsite mitigation wetlands shall be constructed and vegetated as described in Section 4 of the MMP. Documentation of the completion of the required mitigation measures shall be included in the Project’s As-Built Report (See Condition 16), including pre- and post-construction photographs from the photo-documentation points required in Condition 15. Maintenance and monitoring of the onsite mitigation wetlands shall be implemented as described in MMP Sections 5 and 6 until the year 5 success criteria in MMP Sections 6.5.1 and 6.5.2 and Tables 2 and 3 in the body of this Certification are attained. Success of the mitigation wetlands shall be determined by Water Board staff;

20. Monitoring Vegetation at the Mitigation Site. Plant cover, plant diversity, and plant height shall be monitored for at least five years, as specified in MMP Sections 6.6.2 through 6.6.5. Only plants that have survived for two years without irrigation may be used to demonstrate compliance with the final vegetation performance standards in Tables 2 and 3 in the body of this Certification. If year 5 success criteria are not achieved, dead plants must be replaced in kind, unless the Permittee demonstrates that the site is not conducive to survival of a plant species, in which case alternate native wetland or riparian plant species may be used, upon obtaining the approval of the Water Board’s Executive Officer.

Replacement plantings must be made within one year of plants failing to meet the specified performance standards. Replacement plants shall be mailto:RB2-401Reports@waterboards.ca.gov

Water Quality Certification and Order CIWQS Place ID 867849 monitored for five years from the date of replanting. Replacement plants are subject to the same performance criterion as the initial plantings;

21. Monitoring Tidal Inlet Stability and Topographic Changes at Mitigation Site. The stability of the tidal inlet channel and topographic changes in the mitigation wetlands shall be monitored as described in MMP Section 6.6.6. If monitoring indicates excessive changes in topography that may compromise the success of the mitigation wetlands or the long-term stability of the tidal inlet channel, the Permittee shall coordinate with the Water Board to evaluate potential sources of the instability and propose remedial actions. If deemed necessary by the Water Board, remedial actions shall be implemented and funded by the Permittee;

22. Monitoring of Invasive Species at Mitigation Sites. During the initial 5-year monitoring period, the mitigation wetlands shall be surveyed for non-native plant species that are rated as “High” risk to the health of wild lands by the California Invasive Plant Council (http://www.cal-ipc.org/paf/) as described in MMP Sections 6.6.2 and 6.6.4, and these species shall be removed to maintain cover by invasive species at five percent or less.

MMP Section 5.5.2 lists other non-native species that are not rated “High” but are known to be invasive in the area; these species shall also be controlled. Weed control activities may include mowing, cutting, hand-removal and/or herbicide application. Trash and other undesirable debris shall be removed from the mitigation area throughout the initial monitoring period. Weed control and debris management, including the names and quantities of any herbicides used at the Project site, shall be summarized in the monitoring report for that year (See Condition 23);

23. Monitoring Reports. Monitoring reports shall be submitted to the Water Board by January 31 following years 1 through 5 after construction and planting of the mitigation wetlands. The reports shall include information on the percent cover by plants, plant diversity, plant height, percent cover by invasive species, topographic changes in the wetlands, and the stability of the tidal inlet. Reports shall summarize each year’s monitoring results (See Conditions 20, 21, and 22), including the need for any remedial actions (e.g. re-planting or tidal inlet stabilization), and include all information specified in MMP Section 6.7. Reports shall describe any maintenance activities performed in the prior year, including, but not limited to, any removal of debris from the wetlands, any stabilization measures implemented in the tidal inlet, management of invasive plant species, and replanting or reseeding of vegetation. The reports shall compare data to previous years and detail progress towards meeting year 5 success criteria in Tables 2 and 3 in the body of this Certification. At the end of year 5, a comprehensive final report shall be prepared that includes summaries of the monitoring data, representative photos, and maps.

Monitoring reports and the comprehensive final report shall include http://www.cal-ipc.org/paf/

Water Quality Certification and Order CIWQS Place ID 867849 photographs from the 10 photo-documentation points specified in Condition 15. The final report shall document if the mitigation wetlands have attained the year five success criteria. If a performance standard is not met in any of the monitoring years, or if the final success criteria are not met at the end of year 5, the Permittee shall work with the Water Board to prepare an analysis of the cause of the failure. If deemed necessary by the Executive Officer of the Water Board, remedial actions shall be implemented, including extension of the monitoring period until the year 5 success criteria are met. Success of mitigation shall be determined by Water Board staff.

24. Long-Term Management of the Onsite Mitigation Wetlands Long-term maintenance and management of the mitigation wetlands shall be the responsibility of the Permittee. The long-term maintenance and management requirements are presented in MMP Section 7;

25. Conservation Land Use Agreement for the Onsite Mitigation Wetlands To preserve the onsite mitigation wetlands in perpetuity, the Corps and the Permittee shall sign the Conservation Land Use Agreement between the Department of Veterans Affairs and the United States Army Corps of Engineers (CLUA). The text of the CLUA is in Att. B. No later than August 1, 2020, the Permittee shall provide the Water Board’s Executive Officer with a copy of the CLUA that has been signed by authorized representatives of the VA and the Corps. Any changes to the text of the CLUA in Att. B must be submitted to the Executive Officer of the Water Board for review and approval before the revised CLUA is signed;

6.6 Post-Construction Stormwater Treatment

26. Project Compliance with the MRP. The Permittee shall ensure the

Project fully complies with Provision C.3 of the Municipal Regional Stormwater National Pollutant Discharge Elimination System (NPDES) Permit (MRP) as described in the body of this Certification. The Permittee shall construct the stormwater treatment infrastructure illustrated in the Sheets titled Stormwater Management Plan C101, Stormwater Management Plan C102, and RWQCB Stormwater Management Concept Plan in Att. A. The Permittee shall implement Storm Water Treatment System Operation and Maintenance Plan for VA Multi-Specialty Outpatient Clinic Columbarium, and Conservation Management Office Alameda Point, Alameda, California (Corps, Sacramento District, December 17, 2020). The stormwater treatment measures at the Project site shall be constructed and operational in the first rainy season in which new or redeveloped impervious surfaces are created that drain to a stormwater treatment measure, following the stabilization of soil within the drainage area tributary to the stormwater treatment measure.