WDR_WQC_2020_to_2024_Final signed.pdf

CALIFORNIA REGIONAL WATER QUALITY CONTROL BOARD

SAN FRANCISCO BAY REGION

ORDER NO. R2-2020-0011

REISSUED WASTE DISCHARGE REQUIREMENTS and WATER QUALITY CERTIFICATION for:

U.S. ARMY CORPS OF ENGINEERS, SAN FRANCISCO DISTRICT

SAN FRANCISCO BAY FEDERAL CHANNEL MAINTENANCE DREDGING

PROGRAM, 2020 THROUGH 2024

The California Regional Water Quality Control Board, San Francisco Bay Region (Water Board), finds that:

Purpose

1. This Order constitutes Waste Discharge Requirements (WDRs) and Water

Quality Certification (Certification) for the U.S. Army Corps of Engineers, San Francisco District’s (USACE) federal navigation channel maintenance dredging program in the San Francisco Bay Area and for disposal of dredged material created by these activities over the January 2020 through December 2024 five-year period. USACE previously implemented San Francisco Bay Area navigation maintenance dredging under WDRs and Water Quality Certification Order No.

R2-2015-0023 issued for a five-year period starting in 2015. To fully address potentially significant impacts of hydraulic dredging, i.e., entrainment of fish species listed as threatened or endangered under State and federal endangered species acts, this Order conditions dredging activities to reduce the use of hydraulic suction hopper dredges in San Francisco Bay.

Scope

2. USACE maintains the navigability of federally-authorized channels at the entrance to and in San Francisco Bay. USACE removes accumulated sediment (primarily silt and clay) by hydraulic (e.g., self-propelled hopper, hydraulic cutter head) or mechanical (e.g., clamshell) dredges and typically disposes of the dredged material by either self-propelled hopper, dump scow, or by use of a pipeline to transport material to beneficial reuse sites.

3. This Order applies only to maintenance dredging, which is performed on a periodic basis to previously authorized depths and removes recently deposited materials. This Order does not apply to “new work” dredging, which removes material to new authorized depths and may involve dredging consolidated materials or historically-contaminated materials.

4. For the five-year period covered by this Order, USACE proposes to perform maintenance dredging at several locations in the Bay Area (Figures 1 - 11).

Based on the range of volumes that USACE has proposed for planning purposes over the next five years (Tables 1 and 2), the maximum total dredging volume within San Francisco Bay is 12.9 million cubic yards (mcy) and the maximum

U. S. Army Corps of Engineers Maintenance Dredging 2020-2024 Reissued Waste Discharge Requirements & Water Quality Certification total dredging volume in the San Francisco Main Ship Channel (MSC) west of the Golden Gate, outside San Francisco Bay is 2.25 mcy.

Long-Term Management Strategy for Disposal of Dredged Material

5. The Water Board and USACE are agencies that participate in the Long-Term

Management Strategy (LTMS) for the Placement of Dredged Material in the San Francisco Bay Region. Other agencies participating in LTMS are U. S. EPA, the San Francisco Bay Conservation and Development Commission (BCDC), and the California State Lands Commission (CSLC). These LTMS agencies evaluated alternative management options for disposal and reuse of dredged sediment over a 50-year planning horizon in a Policy Environmental Impact Statement/Programmatic Environmental Impact Report (EIS/EIR) completed in October 1998. The EIS/EIR indicated that dredged material disposal may have adverse impacts on the beneficial uses of the waters of San Francisco Bay and that in-Bay disposal should be reduced from historical levels.

6. The LTMS agencies determined that the preferred alternative is to reduce disposal in the Bay to a long-term average of 1.25 mcy or less per year, with approximately 80 percent of dredged sediment to be targeted for beneficial reuse or out-of-Bay disposal and only 20 percent targeted for in-Bay disposal.

This long-term goal can be accomplished by maximizing beneficial reuse of dredged material suitable for habitat restoration along the Bay margins and disposing suitable dredged material outside the Bay only when beneficial reuse is not practicable. As the science and knowledge regarding climate change and the resulting rise in sea levels has grown, it is now recognized that the low-lying areas of the Bay, which were once historical marshes, are in jeopardy of being inundated both by rising sea levels and storm surges that are occurring more frequently and at greater intensity than previously experienced. In addition, in the mid-2000s, scientists from the U.S. Geological Survey identified a significant reduction in suspended sediment loading from the Sacramento-San Joaquin river system. Less sediment in suspension and circulation within the Bay impairs the ability of shorelines, mudflats, and tidal wetlands to withstand erosion and inundation, especially as sea level rises.

The Water Board therefore finds that it is in the public interest to encourage beneficial reuse of suitable dredged material as one component of regional adaptation to climate change and reduced suspended sediment loading to the Bay.

7. Specific guidance for implementing the LTMS long-term goal of reducing in- Bay disposal is described in the LTMS Management Plan (Management Plan), approved in July 2001 by the LTMS Executive Committee. To achieve the goal, the Management Plan included an in-Bay disposal target of 1.25 mcy or less annually over a three-year period. To allow time for planning, budgeting, and creating alternatives to in-Bay disposal, the Management Plan established a 12-year transition period for achieving the in-Bay disposal target. The transition period’s disposal volume limits were voluntary as long as the long-term goal was met overall. Public assurance that in-Bay disposal would in fact decrease was provided by language identifying when strict volume allocations to individual dredgers would be triggered (i.e., a disposal allocation trigger).

The transition period successfully concluded in 2012 with in-Bay disposal targets met every three years as described in the Management Plan.

USACE is the largest dredger in the Bay Area. Efforts by USACE to reduce in-Bay disposal are critical to successful implementation of the LTMS long-term goal. In keeping with the LTMS long-term goal, USACE must reserve sufficient monthly capacity at in-Bay disposal sites for smaller non-USACE projects. The 1.25 mcy annual in-Bay disposal target allocates 0.25 mcy/year to “small” dredging projects, defined in the Management Plan as those projects that generate less than 50,000 cy per year on average with a design depth of less than -12 feet MLLW, leaving the remaining 1.0 mcy of the disposal goal plus a 0.25 mcy “contingency volume” to be split between USACE and the medium-sized maritime industry dredgers. If the total average annual in-Bay disposal volume from the prior three-year averaging period exceeds 1.5 mcy (1.25 mcy target plus 0.25 mcy contingency), both the Management Plan and the Basin Plan direct the Water Board to consider imposition of mandatory in-Bay disposal allocations for all dredgers.

Since transitioning to the final in-Bay disposal target in 2012, USACE’s dredging has accounted for approximately 70 percent of the total volume of sediment dredged in San Francisco Bay by all dredgers. USACE’s combined average annual in-Bay disposal volume over the first two post-2012 LTMS averaging periods (2013 – 2015 and 2016 - 2018) was 0.816 mcy per year.

Neither the 1.5 mcy average annual in-Bay disposal allocation trigger nor the

1.25 mcy average annual in-Bay disposal target was exceeded during these averaging periods. For years 2020 through 2024, we expect USACE to continue to maintain an average annual in Bay disposal volume of 0.816 mcy or less without resulting in exceedance of the in-Bay disposal allocation trigger. The total not to exceed in-Bay disposal volume for this Order is therefore 4.08 mcy (calculated as 0.816 mcy times five years).

This Order authorizes the Executive Officer to consider allowing USACE to exceed 4.08 mcy of in-Bay disposal provided that the additional volume will not result in an exceedance of the 1.5 mcy allocation trigger and also that 50 percent of the excess volume will be beneficially reused at an aquatic habitat creation or restoration project. This will ensure that the allocation trigger will not be exceeded. It is also consistent with the LTMS goals of maximizing the use of dredged material as a resource. In addition, it takes into consideration the USACE’s disproportional use of in-bay disposal by providing 10 percent more than the minimum beneficial reuse percentage in the preferred alternative in the EIS/EIR for the LTMS Management Plan (Alternative 3, LTMS EIS/EIR), which included a minimum of 40 percent beneficial reuse (LTMS Management Plan, p. 1-12). USACE’s disproportional use of in-bay disposal reduces the availability of in-bay disposal for other dredgers thereby increasing their burden to achieve a minimum of 40 percent beneficial reuse.

Thus, requiring USACE to beneficially reuse 10 percent more than the minimum beneficial use goal for this excess volume will offset the loss of in-bay disposal volume for other dredgers by providing a greater proportion of dredge material for beneficial reuse.

Dredging Projects Summary

8. USACE’s maintenance dredging program provides for maintenance of ten federal navigation channels inside San Francisco Bay, including six channels dredged annually or biennially and four channels with less frequent dredging cycles. These ten channels have a combined surface area that equates to approximately 2.22 percent of the total surface area of San Francisco Bay.

During each fiscal year or every other year from 2020 to 2024, USACE plans to dredge the channels most critical to the region’s maritime trade and to regional and national economies: Oakland Harbor, Richmond Outer Harbor, Richmond Inner Harbor, Suisun Bay and New York Slough, Pinole Shoal (San Pablo Bay), Redwood City Harbor (not including the San Bruno Channel).

Other channels that USACE may dredge once at some point during the next five years, if funding becomes available, include the San Rafael (Inner) Canal and Across the Flats, the Napa River (upper and lower reaches), Petaluma River (upper portion and Across the Flats), and the San Bruno Channel. Each of these channels is either due or overdue for dredging.

USACE also annually dredges the Main Ship Channel outside San Francisco Bay, which is not part of the LTMS Program. Although the eastern portion of the channel is within the seaward limit of State submerged lands (three nautical miles from the coastline) and is therefore within Water Board jurisdiction, dredging has not taken place in this portion of the channel over the past 20 years and USACE does not expect this condition to change during the next five years.

The general locations of the channels are depicted collectively in Figure 1. The channel boundaries are more precisely shown on the project maps provided in Figures 2 - 10. Since this Order is a five-year WDR/Certification, the actual shoaling locations are not yet known. Dredging will be confined within the channel boundaries shown in Figures 2 - 10 and shall not exceed the project depth, as shown in Tables 1 and 2, plus an over dredge depth of 2 feet.

Placement of dredge material will be confined to the boundaries of the placement sites depicted in Figures 1 - 10.

Table 1 summarizes USACE’s 2020 - 2024 dredging activities under the LTMS Program and Table 2 summarizes USACE’s 2020 - 2024 dredging of the Main Ship Channel, including maximum estimated dredging volumes, the Water Board’s preferred placement sites, the federal standard placement sites, and alternate placement sites. The volume estimates are based on historical data.

Table 1. 2020 – 2024 San Francisco Bay Dredging Project Summary

Project Maintenance

Depth (feet below

MLLW)1

Dredge Type

Expected Dredging

Frequency in 2020-

Maximum Planning

Volume per Dredge Episode

(cy)

Water Board Preferred

Placement Site

Federal Standard

Placement Site2

Alternate

Placement Site

Richmond Inner Harbor 38 Clamshell-

Bucket Annual 350,000 Habitat

Restoration Beneficial

Reuse

SF-DODS

Upland Beneficial

Reuse

Richmond Outer Harbor 45

Clamshell- Bucket or Hopper*

Annual (Biennial)

350,000 (700,000)

Habitat Restoration Beneficial

Reuse SF-11 Other In-Bay

Site (SF-10)

Oakland Inner and Outer Harbor 50 Clamshell-

Bucket Annual 950,000 Habitat

Restoration Beneficial

Reuse

SF-DODS

Upland Beneficial

Reuse

Pinole Shoal 35 Clamshell- Bucket or Hopper*

Annual (Biennial)

300,000 (600,000)

Habitat Restoration Beneficial

Reuse SF-10 Other In-Bay

Site (SF-11)

Suisun Bay Channel and New York Slough3,4

35 Clamshell- Bucket Annual 200,000

Habitat Restoration Beneficial

Reuse SF-16 Other In-Bay

Site (SF-9)

Redwood City Harbor (Harbor Channel) 30 Clamshell

Bucket

Twice (2021 & 2023)

300,000

Habitat Restoration Beneficial

Reuse

SF-11 SF-DODS

Project Maintenance

Depth (feet below

MLLW)1

Dredge Type

Expected Dredging

Frequency in 2020-

Maximum Planning

Volume per Dredge Episode

(cy)

Water Board Preferred

Placement Site

Federal Standard

Placement Site2

Alternate

Placement Site

Redwood City Harbor (San Bruno Shoal) 30 Clamshell or

Hopper Once 16,000 Habitat

Restoration Beneficial

Reuse

SF-11 SF-DODS

Petaluma River Channel 8

Hydraulic Cutterhead-

Pipeline Once 350,000

Habitat Restoration Beneficial

Reuse

Shollenberger Park (Upland

Sponsor- Provided Site)

Upland Beneficial

Reuse

Petaluma River (Across the Flats) 8 Clamshell Bucket Once 250,000

Habitat Restoration Beneficial

Reuse

SF-10

Upland Beneficial

Reuse

Hopper Dredge Sea Trials NA Hopper Up to five times 12,000 Beach

Nourishment Beneficial

Reuse

SF-11 SF-8

Lower Napa River Channel (Mare Island Strait Causeway to Asylum Slough)

95 Clamshell-Bucket Once 13,000 Habitat

Restoration Beneficial

Reuse

Upland (Sponsor- Provided)

Other Upland Site

Project Maintenance

Depth (feet below

MLLW)1

Dredge Type

Expected Dredging

Frequency in 2020-

Maximum Planning

Volume per Dredge Episode

(cy)

Water Board Preferred

Placement Site

Federal Standard

Placement Site2

Alternate

Placement Site

Upper Napa River Channel (Asylum Slough to Third Street)

96 Clamshell- Bucket Once 55,000

Habitat Restoration Beneficial

Reuse

Upland (Sponsor- Provided)

Other Upland Site

San Rafael Creek Channel

6 (Inner Canal); 8

(Across the Flats)

Clamshell- Bucket

Once 87,000 Habitat

Restoration Beneficial

Reuse SF-10 Other In-Bay

Site (SF-11)

Notes:

* Both Richmond Outer Harbor and Pinole Shoal cannot be dredged with a hopper in the same year - see Provision 9.

1 Typical 2-foot overdredge allowances beyond these depths are not shown.

2 The federal standard is defined as the least-costly dredged material disposal or placement alternative consistent with sound engineering practices, and meeting the environmental standards established by the 404(b)(1) evaluation process or ocean dumping criteria (33 C.F.R. § 335.7).

3 Aside from regularly scheduled maintenance of this navigation project, USACE would take urgent action outside the work window, as needed, to remove the hazardous shoaling at Bulls Head Reach.

4 Due to rapid shoaling at Bulls Head Reach, this portion of the Suisun Bay Channel may be advance maintenance dredged by up to 4 feet, plus an additional 2 feet of allowable overdepth.

5 The authorized depth is -15 feet MLLW but infrequent maintenance has caused some areas to be as shallow or shallower than -10 feet MLLW. To avoid conversion of delta smelt shallow water habitat (-10 feet MLLW or shallower), the project will be dredging to 9 feet MLLW plus 1 foot of overdepth for its entire length per the terms of the U.S. Fish and Wildlife Service’s Programmatic LTMS Biological Opinion.

6 The authorized depth is -10 feet MLLW but infrequent maintenance has caused some areas to be as shallow or shallower than -10 feet MLLW. To avoid conversion of delta smelt shallow water habitat (-10 feet MLLW or shallower), the project will be dredging to 9 feet MLLW plus 1 foot of overdepth for its entire length per the terms of the U.S. Fish and Wildlife Service’s Programmatic LTMS Biological Opinion.

cy = cubic yards mcy = million cubic yards SF-9 = Carquinez Strait placement site

SF-10 = San Pablo Bay placement site SF-11 = Alcatraz Island placement site SF-16 = Suisun Bay placement site

SF-DODS = San Francisco Deep Ocean Disposal Site (55 miles west of Golden Gate)

Table 2. Main Ship Channel Dredging Summary

Project Maintenance Depth (feet below

MLLW)1

Dredge Type Expected Dredging

Frequency in 2020-2024

Maximum Planning

Volume per Dredge Episode

Water Board Preferred

Placement Site

Federal Standard

Placement Site2

Alternate

Placement Site

San Francisco Harbor – Main Ship Channel

55 Hopper Annual 450,000 Ocean Beach Onshore SF 8 SF 17

Notes:

1 Typical 2-foot overdredge allowances beyond these depths are not shown.

2 The federal standard is defined as the least-costly dredged material disposal or placement alternative consistent with sound engineering practices, and meeting the environmental standards established by the 404(b)(1) evaluation process or ocean dumping criteria (33 C.F.R. § 335.7).

Ocean Beach Onshore = Onshore Ocean Beach placement site SF-8 = San Francisco Bar Channel Disposal Site SF-17 = Ocean Beach placement site (near shore site, includes the Ocean Beach demonstration site)

Placement Sites for Dredged Material

9. It is LTMS’ goal that sediment dredged from San Francisco Bay be beneficially reused for a variety of purposes, such as wetland restoration, levee maintenance, or construction fill. Existing fully permitted beneficial reuse sites include the Montezuma Wetlands Restoration Project (regulated by Water Board Order No. R2-2012-0089) and the Cullinan Ranch Restoration Project (regulated by Water Board Order No. R2-2010-0108) with remaining sediment placement capacities of approximately 10 mcy and 1.5 – 1.9 mcy, respectively (Figures 1, 5, 6, and 8). The Eden Landing Ecological Reserve Wetland Restoration Project Phase II and the Bel Marin Keys Unit V expansion of the Hamilton Wetland Restoration Project are two other wetland restoration projects currently in the permitting phase and expected to be ready to receive sediment within the next five years (Figures 7 and 9). The dredged sediment reuse capacities of these two sites are 7.2 mcy and 9.5 mcy, respectively. At their own discretion, dredging contractors or the project sponsors may propose to use other permitted beneficial reuse locations. All necessary environmental documentation must be completed for a site prior to it receiving any dredged material.

Disposal in the Bay consistent with the goal occurs at four designated aquatic disposal sites (Figure 1): the Alcatraz Island Disposal Site (SF-11), the San Pablo Bay Disposal Site (SF-10), the Carquinez Strait Disposal Site (SF-09), and the Suisun Bay Disposal Site (SF-16). Ocean disposal for Bay dredged material occurs at the San Francisco Deep Ocean Disposal Site (SF-DODS), about 55 miles (48 nautical miles) west of the Golden Gate and thus beyond the three-mile offshore limit of Water Board jurisdiction. Under the federal Marine Protection, Research and Sanctuary Act, U.S. EPA must concur with disposal at SF-DODS.

Sand dredged from the San Francisco MSC may be placed for beneficial reuse (nourishment of the San Francisco littoral cell to help combat erosion at Ocean Beach) at the easternmost portion of the San Francisco Bar Disposal Site (SF-8) (Figure 2), within the three nautical mile limit of Water Board jurisdiction.

Pre-site-designation studies concluded that the area would be dispersive, meaning that waves would spread the sand shoreward to the surf zone and beach at such a rate that accumulation would be minimal. However, surveys indicate that spreading occurs at a much slower rate than expected and that underwater shoals impair safe operation of hopper dredges during rough seas.

USACE therefore limits use of SF-8 to the extent feasible. USACE is currently conducting a beach nourishment beneficial reuse pilot demonstration study at the Ocean Beach Near Shore Demonstration Site, which is encompassed by the future SF-17 placement site (SF-17), in waters of the Pacific Ocean adjacent to the south-of-Sloat-Boulevard stretch of Ocean Beach (Figure 2). SF-17 is located where waves can potentially feed sediment toward the southern reach of Ocean Beach, which may ultimately help mitigate ongoing shoreline erosion in the area that threatens significant municipal infrastructure, including segments of the Great Highway and major sewer lines running underneath and alongside it.

USACE and the U.S. EPA are in the process of formally designating SF-17 as a permanent nearshore placement site for the beneficial use of clean dredged sand under 40 CFR Part 230.8 for Advance Identification of Disposal Sites and section 404 of the Clean Water Act.

Because placement of dredged sediment at beneficial reuse sites is generally more expensive than in-Bay or deep ocean disposal, the Water Board recognizes that additional funding for beneficial reuse may need to be provided by sources outside USACE such as local project sponsors, State appropriations, or granting agencies like the San Francisco Bay Restoration Authority.

Review of Dredging Episodes

10. The Water Board participates in the Dredged Material Management Office

(DMMO); a working group with representatives of the State and federal agencies with regulatory authority over Bay Area dredging projects. Staff representatives of the Water Board, USACE, U.S. EPA, BCDC, and CSLC meet regularly to jointly review dredging projects and make consensus-based recommendations to their respective agencies about the suitability of sediments for proposed placement sites based on sediment testing conducted according to DMMO testing requirements. Material proposed to be dredged and placed at ocean, inland aquatic, or beneficial reuse sites requires sediment characterization to predict the environmental impacts associated with dredging and dredged material placement activities. The objective of the sediment testing requirements is to ensure that disposal of dredged material at designated disposal sites occurs without causing unreasonable degradation to the surrounding environment.

Generally, sediments are tested for physical and chemical attributes and/or the potential for biological toxicity.

Representatives from the California Department of Fish and Wildlife (CDFW), the U.S. Fish and Wildlife Service (USFWS) and the National Marine Fisheries Service (NMFS) also participate in the DMMO in an advisory capacity. Each DMMO agency retains its independent decision-making authority, but the group has significantly reduced project review time by concurrent consideration of projects. USACE handles the logistics for the operation of the DMMO.

This Order requires that dredging episodes carried out under this Order will be reviewed by the DMMO for a recommendation on the suitability for disposal or beneficial reuse of the dredged material. Each dredging episode must be approved in writing by Water Board staff.

Barring and Knock-down Dredging

11. Barring as part of a dredging episode: USACE plans to implement “barring” as a routine part of dredging episodes to smooth out high spots as needed after dredging has occurred. This method involves using a tug to pull a weighted blade across the channel bottom. As the blade encounters material, it scrapes the material into the adjoining areas with deeper depressions, redistributing the shoaled material within the project area. Barring will be restricted to the channel footprint and the project depth, including the over dredge depth allowance. If barring were not utilized as part of dredging episodes, the vessel operator would likely have to dredge below project depth in certain areas in order to ensure safe navigation, resulting in an increased volume of material dredged and decreasing overall efficiency.

Knock-down performed in lieu of dredging: Separate from barring, which is implemented at the end of dredging episodes, USACE anticipates performing several “knock-down” events in lieu of conducting full dredging episodes. Knock-downs would use the same equipment and procedures as barring but would apply to isolated shoals or high-spots rather than an entire channel. Knock-downs are most useful when time constraints may not allow for normal dredging or when a shoal threatening navigation covers a small area of a project area that is otherwise at or below its permitted depth. Conducting separate knock-down operations is often more efficient than mobilizing dredging equipment and transporting the material to a disposal site. Knock-down events occurring separately from full dredging episodes, or in combination with a dredging episode occurring in a different location within the same channel, will be subject to the same coordination with the DMMO as full dredging episodes. The volume of material above project design depth to be knocked down under these separate operations is not anticipated to exceed 15,000 cy per year in each deep draft channel. Each knock-down that is a stand-alone event, and not associated with a dredging episode, must be approved by Water Board staff. Depending on the volume of sediment, contaminant concentrations, and other project-specific details, water quality monitoring may be required and will be coordinated during the episode approval process described in Provision 3 of this Order.

Advance Maintenance Dredging

12. Advance maintenance dredging is utilized in areas where typical shoaling patterns create navigational restrictions on an ongoing basis. Advance maintenance dredging that does not exceed the yearly maximum volume of dredge material shall be allowed and shall be coordinated through the typical DMMO process. Advance maintenance is restricted to areas that exhibit rapid shoaling and the material shall be characterized through the standard DMMO process. If advance maintenance dredging for any channel is expected to exceed the maximum volume shown in Table 1, or reconfiguration of a channel becomes necessary, USACE will notify the Executive Officer pursuant to Provision 2 of this Order.

Emergency Dredging

13. USACE is required to ensure that all navigation channels are dredged to a safe depth. If an area is found to be an unacceptable hazard to life or navigation or threatens to cause an immediate and unforeseen significant economic hardship if corrective action is not taken quickly, USACE may carry out dredging on a limited basis even though that project is not scheduled for dredging. In such cases, an expedited testing and approval process is often necessary. USACE does not anticipate performing more than three emergency dredging episodes consisting of less than 30,000 cy each per year.

The Water Board recognizes the need for expedited review of emergency dredging episodes and expects that USACE will still follow the procedures outlined in Provision 3 of this Order for written approval of emergency dredging episodes.

In atypical conditions, such as after an extraordinary storm event, a shoaling situation may be such an immediate hazard that even an expedited review process is not feasible. The Water Board recognizes that USACE has the authority to remove the immediate hazard without the Executive Officer’s approval pursuant to this Order.

Management of the in-Bay Disposal Sites

14. The in-Bay disposal sites are operated as “dispersive” sites, that is, material disposed of at the sites should be dispersed by currents and tidal flows, and the sites should not accumulate material. USACE is responsible for managing and monitoring the sites. USACE manages the total volume, timing, and locations of disposal at the sites and performs regular bathymetric surveys at the sites to determine whether dredged material is accumulating.

15. In the late 1980s, USACE surveys of the Alcatraz disposal site showed a drastic decline in depth and unexpected bottom topography ("mounding"). USACE changed management practices at the Alcatraz site, directing disposal episodes to specific areas within the disposal site, and reducing the monthly allowable volume of disposal during winter months (USACE Public Notice No. 93-3). Table 3, below, shows the monthly and annual maximum volume targets for all dredgers currently in effect for the in-Bay disposal sites. To minimize water quality impacts associated with in-Bay dredged sediment disposal such as temporary increased suspended solids loading and benthic habitat disruption, Provisions 16 and 17 of this Order require that USACE continue to monitor and manage the disposal sites so that the volume targets in Table 3 are not exceeded.

Table 3. Monthly and Annual Maximum Volume Targets Designated Disposal Site Monthly

Target Volume (cy)

Annual Target

Volume (cy) Alcatraz Island (SF-11)

October – April 400,000 NA May – September 300,000 NA

Carquinez Strait (SF-9) – Any Month

1,000,000 NA

San Pablo Bay (SF-10) – Any Month

500,000 NA

Suisun Bay (SF-16) 200,000

Three-year average of the total in-Bay Disposal Volume

1.25 milliona

Notes a This volume does not include an allowable contingency volume of 250,000 cy per year but does include the 250,000 cy small dredger allowance

Impacts of Dredging and in-Bay Disposal

16. Consultations and Work Windows for Dredging: During the preparation of the

1998 LTMS EIS/EIR, the LTMS agencies initiated State and federal endangered species act (ESA) consultations with CDFW, NMFS, and USFWS for maintenance dredging and disposal projects, covering threatened and endangered species and species of special concern, such as the Pacific herring.

These programmatic consultations reduced the need for consultation on each individual dredging project by establishing programmatic work windows. These programmatic work windows are based on presence/absence information for various sensitive species and establish times and locations where dredging and disposal activities may take place without further consultation.

The programmatic consultations resulted in biological opinions issued by NMFS and USFWS that provide federal endangered or threatened species “incidental take” authorization for projects operating in the environmental work window for their area. This “take authorization” protects the dredger from enforcement action in the event of accidental harm to a listed species resulting from the dredging project. The programmatic biological opinions issued by NMFS and USFWS do not address incidental take of State-listed species. Coordination with CDFW is necessary if take of State-listed species is expected. As a federal agency, USACE is not required to obtain authorization from CDFW for incidental take of State-listed species because there has been no waiver of federal sovereignty with respect to the California Endangered Species Act (CESA). The Water Board, however, as explained further in Finding 18, must comply with CESA when issuing WDRs and water quality certifications.

Beginning in 2011, USFWS required USACE to annually consult on impacts to delta smelt during dredging of Suisun Bay Channel and New York Slough due to documented occurrences of entrainment during monitoring of hopper dredge use in 2011. USACE has not used a hopper dredge in the Suisun Bay Channel and New York Slough since 2014, as required by USFWS in biological opinions it has issued from 2015 forward. USACE proposes using only mechanical clamshell dredges in the Suisun Bay Channel and New York Slough in 2020 through 2024.

In July 2015, NMFS updated its programmatic LTMS biological opinion to include green sturgeon, which was listed as threatened under the federal ESA in 2006.

The updated biological opinion also expanded the salmonid work window to year-round if dredging is conducted with a clamshell dredge and the sediment is placed at a beneficial reuse site, such as a tidal wetlands restoration, that NMFS agrees will provide aquatic habitat benefits for salmonids. Under the updated biological opinion, USACE may opt to dredge certain federal navigation channels with a clamshell dredge outside the work windows and place sediment at a beneficial reuse site without additional consultation with NMFS. All other dredging outside the work window (i.e., hydraulic dredging or clamshell dredging with placement at a non-beneficial reuse site) requires consultation with NMFS and, if applicable, the other resource agencies.

This Order requires that USACE comply with the programmatic LTMS work windows established through consultation with CDFW, NMFS, and USFWS. If USACE proposes dredging outside the established work windows, it must notify the Water Board and implement all applicable mitigation measures established in the programmatic LTMS consultations or individual project consultations.

17. Entrainment of Special-Status including Longfin Smelt and Delta Smelt:

All forms of dredging have the potential to incidentally remove fish and other aquatic life from the environment with the dredged material, a process referred to as entrainment. Animals and plants on top of or embedded in the sediment as well as those in the water column near the dredging apparatus may be entrained. In general, smaller organisms with limited or no swimming capabilities are more susceptible to entrainment. Mechanical dredging is generally accepted to entrain far fewer fish than hydraulic dredging, because much less water is removed along with the sediment. However, it still may remove demersal fish and crustaceans that live in or on the sediment.

Entrained fish are likely to suffer mechanical injury or suffocation during dredging, resulting in mortality. Longfin smelt and delta smelt are not strong swimmers and are presumed susceptible to entrainment in the flow fields created around the intakes of hydraulic suction dredges. Longfin smelt have the potential to occur in any of the project areas in any season. Delta smelt have potential to occur in the portions of the San Francisco Estuary that include the Napa River Channel, San Pablo Bay/Mare Island Strait, and Suisun Bay Channel dredge areas during certain seasons. Delta smelt occur in San Pablo Bay in lower numbers than in the Napa River or Suisun Bay;

however, they may be present in San Pablo Bay in increased numbers during high water outflow years. Delta smelt are not expected to occur in the other federal channels.

Entrainment Study: Over the past two decades, according to CDFW survey data, abundance indices for various life stages of delta smelt have hit record lows, indicating that the species is in imminent danger of extinction. In response, the State elevated its listing status from threatened to endangered in 2010. USFWS listed delta smelt as threatened on March 5, 1993, and designated critical habitat for this species on December 19, 1994. On April 7, 2010, USFWS submitted a 12-month petition finding to reclassify delta smelt as endangered. They found that reclassification is warranted but precluded by other higher-priority listing actions. Similarly, CDFW longfin smelt annual abundance indices from the fall mid-water trawl surveys show that the population has declined 99 percent or more in the last 45 years, with record lows in the past decade. On March 9, 2009, the State Fish and Game Commission listed longfin smelt as threatened under CESA. On April 2, 2012, USFWS released a 12-month review of longfin smelt status in which it concluded that the listing of the longfin smelt as a threatened species is warranted but is currently precluded by other higher-priority listing actions. As a result, longfin smelt is currently a candidate species for listing under the federal ESA.

In 2013, the United States Army Engineer Research and Development Center (ERDC) prepared a modeling study of entrainment of longfin and delta smelt in San Francisco Bay by hydraulic dredges. In the study, the risk of smelt entrainment was assessed by comparing fish abundances in the environment (CDFW monthly trawls described above) to fish collections in entrainment monitoring samples (screened sub-samples of dredged material) collected during dredging by the hopper dredge Essayons in San Francisco Bay in 2010 and 2011. Due to the technical and logistical limitations of sampling on board the working vessel, only a very small fraction, less than one percent of the total volume dredged, was actually sampled.

Modeled estimates of longfin smelt entrainment during hydraulic dredging in 2011 based on 2011 abundance indices are 3,848 for the low entrainment scenario, 6,528 for the medium entrainment scenario, and 10,260 for the high entrainment scenario (up to approximately 8 percent of the median annual population abundance). Modeled estimates of delta smelt entrainment during hydraulic dredging in 2011 based on 2011 abundance indices are 394 for the low entrainment scenario, 1,444 for the medium entrainment scenario, and 3,694 for the high entrainment scenario (up to approximately 29 percent of the median annual population abundance). Many factors are associated with the accuracy of these projections. The small sample size of entrained fish (18 longfin smelt and 4 delta smelt), combined with the low percentage of dredged material sampled, result in a high degree of uncertainty as to the accuracy of the entrainment estimates.

2016-2019 Entrainment Monitoring: Entrainment monitoring aboard the hopper dredge Essayons took place under the previous Order R2-2015-0023 in June, September, and October 2016; June and November 2017; June and October 2018; and in August 2019. No delta smelt were entrained in the monitoring apparatus during these monitoring events, most likely because the Essayons dredged in areas where the salinity exceeded the tolerance limit of delta smelt. However, monitoring during this period demonstrated that entrainment of longfin smelt occurred.

18. Compliance with CESA: As a federal agency, USACE is not required to obtain authorization from CDFW for incidental take of State-listed species because there has been no waiver of federal sovereignty with respect to CESA. The Water Board, however, must comply with CESA when issuing WDRs and water quality certifications. In a letter to CDFW dated February 13, 2014, the Water Board requested guidance on the significance of entrainment impacts to special status fish species and on appropriate mitigation measures.

In its March 14, 2014, reply to the Water Board (attached), CDFW indicated that impacts would be significant. It noted the ERDC estimates of entrainment and stated that “the Project, as proposed, would substantially reduce the number of an endangered, rare, or threatened species.” To reduce dredging-related impacts to special status fish species to a less-than-significant level, CDFW recommended reducing hopper dredging to a minimum in San Francisco Bay and implementing the avoidance, minimization, and mitigation measures listed below.

Fish and Game Code section 2053 states "the policy of the State that State agencies should not approve projects … which would jeopardize the continued existence of any endangered species … if there are reasonable and prudent alternatives available consistent with conserving the species.” This Order includes the measures identified by CDFW to avoid, minimize, and mitigate for entrainment impacts, consistent with conserving the species.

Avoidance, Minimization, and Mitigation Measures for Entrainment Impacts: Based on the ERDC entrainment study and guidance from CDFW, the Water Board has determined that implementation of the following measures combined with minimization of hopper dredge use in San Francisco Bay and compensatory mitigation, as required under Provisions 9 and 10, will mitigate potential entrainment impacts to a less-than-significant level:

a. No dredging will occur in water ranging from 0 to 5 parts per thousand salinity between December 1 and June 30.

b. USACE will coordinate with the appropriate regulatory and resource agencies to perform compensatory mitigation for hydraulic dredging anywhere when water temperature is below 22.0 degrees Celsius.

c. USACE will implement a worker education program for listed fish species that could be adversely impacted by dredging. The program will include a presentation to all workers on biology, general behavior, distribution and habitat needs, sensitivity to human activities, legal protection status, and project-specific protective measures.

d. Pump priming, drag head clearing, and suction of water at the beginning and end of each hopper load will be conducted within three feet of the seafloor.

e. Hopper drag head suction pumps will be turned off when raising and lowering the drag arms from the seafloor.

f. Hydraulic hopper dredging in Suisun Bay will be completed between August 1 and September 30 to avoid impacts to spawning adult longfin and delta smelt.

g. Hydraulic hopper dredging in Central Bay (Richmond Outer Harbor) and San Pablo Bay (Pinole Shoal) will be completed between August 1 and November 30 to avoid impacts to young-of-the-year and spawning adult longfin smelt.

h. The drag head, cutterheads, and pipeline intakes will remain in contact with the seafloor during suction dredging.

i. The drag head water intake doors will be kept closed to the maximum extent practicable in locations most vulnerable to entraining smelt. In circumstances when the doors need to be opened to alleviate clogging, the doors will be opened incrementally (i.e., the doors will be opened in small increments and tested to see if the clog is removed) to ensure that doors are not fully opened unnecessarily.

19. The Water Board has implemented the San Francisco Estuary Regional Monitoring Program for Trace Substances (RMP) since 1992. The RMP is a coordinated and comprehensive long-term monitoring program with the goal of monitoring water and sediment quality to provide the scientific foundation for managing and improving the health of the San Francisco Bay aquatic ecosystem.

Additionally, the RMP provides for special and pilot studies of interest to program participants. USACE is a participant in the RMP and contributes to the program by funding the United States Geological Survey (USGS) to monitor suspended sediments at an array of locations in the Bay. This monitoring has and will continue to improve understanding of sediment transport processes and create a comprehensive database for various numerical modeling efforts.

CEQA

20. California Environmental Quality Act (CEQA): The Board, together with the

USACE, prepared a joint Final Environmental Assessment/Environmental Impact Report for Maintenance Dredging of the Federal Navigation Channels in San Francisco Bay Fiscal Years 2015 – 2024 (FEIR). The Board adopted and certified the FEIR on May 13, 2015, when it adopted waste discharge requirements and water quality certification Order No. 2015-0023 for the 2015 to 2019 period of maintenance dredging activities. The FEIR analyzed maintenance dredging activities and disposal through 2024 and the project authorized by this Order is within the scope of the FEIR. The Board has considered the FEIR, which considered four alternatives:

· No Project Alternative - USACE would conduct maintenance dredging practices for the projects it maintains in the Bay, which include hydraulic suction hopper dredging in three channels inside the Bay (Suisun Bay/New York Slough, Pinole Shoal, and Richmond Outer Harbor) with implementation of all but four of the avoidance, minimization, and mitigation measures for entrainment impacts to longfin smelt and delta smelt listed in Finding 18 and Provision 11.

· Proposed Project Alternative - Dredging and placement would be conducted as under the No Project Alternative. Also, USACE would implement four additional avoidance, minimization, and mitigation measures for entrainment impacts to longfin smelt and delta smelt (measures f, g, h, and i in Finding 18 and Provision 11) and purchase 0.92 acre mitigation credit at the Liberty Island Conservation Bank, or other approved site, annually for potential impacts to listed species. Provision 10 includes the details on calculation of this mitigation credit.

· Reduced Hopper Dredge Use Alternative 1 (MSC and One In-Bay Channel) -The government hopper dredge Essayons, or similarly-sized hopper dredge, would only be used to dredge the MSC and a maximum of one in-Bay federal channel, either the Richmond Outer Harbor or the Pinole Shoal Channel, annually. The channel not selected as the additional hopper dredge channel (i.e., either Pinole Shoal or Richmond Outer Harbor) would be dredged with a mechanical dredge. Suisun Bay/New York Slough Channel would be dredged with a mechanical dredge under this alternative, instead of a hopper dredge. USACE would purchase mitigation credit for entrainment impacts to listed smelt species during hopper dredging in Pinole Shoal or Richmond Harbor as described in the Proposed Project Alternative.

· Reduced Hopper Dredge Use Alternative 2 (MSC only, No In-Bay channels) - The government hopper dredge Essayons, or similarly-sized hopper dredge, would be used to dredge the MSC. Pinole Shoal, Richmond Outer Harbor, and Suisun Bay/New York Slough Channel would be dredged with a mechanical dredge under this alternative, instead of a hopper dredge. All other dredging, placement activities would be as described for the Proposed Action/Project.

The FEIR concluded that the Proposed Project Alternative would have significant effects related to the entrainment of delta smelt and longfin smelt. A public agency may not approve a project for which an environmental impact report has been prepared unless either the project will not have a significant effect on the environment or the agency has eliminated or substantially lessened all significant effects where feasible and determined that any remaining unavoidable significant effects are acceptable due to overriding concerns. (Cal. Code Regs., tit. 14, § 15092, subd. (b).) Information in the record indicates that both Alternative 1 and Alternative 2, which entail reduced hopper dredging, will substantially lessen the significant environmental effects of the Proposed Project Alternative analyzed in the FEIR. The FEIR concludes that both of these alternatives will reduce the impacts to delta smelt and longfin smelt to a less than significant level; all other impacts would be less than significant with mitigation. This is also consistent with CDFW’s March 14, 2014, memorandum to the Water Board stating that impacts could be made less than significant by reducing hopper dredging to a minimum, implementing the other avoidance, minimization, and mitigation measures identified in Finding 18 and Provision 11, and implementing the compensatory mitigation approach described above. There is no information in the record that indicates either Alternative 1 or Alternative 2 is infeasible. For this reason, this Order permits either Alternative 1 or 2.

Since this Order authorizes Alternatives 1 and 2, it will not have a significant impact on the environment. Specifically, the following potential significant impacts to delta smelt and longfin smelt have been reduced to less than significant as follows:

Impact 3.6-5: Potential Substantial Adverse Effects and Cumulative Impacts to Delta Smelt from Entrainment Entrainment of delta smelt could occur during hopper dredging. They are not strong swimmers and are presumed susceptible to entrainment in the flow fields created around the intakes of hydraulic suction dredges. Delta smelt have potential to occur in the portions of the San Francisco Estuary that include the Napa River Channel, San Pablo Bay/Mare Island Strait, and Suisun Bay Channel dredge areas during certain seasons.

Findings: Changes or alterations have been required in, or incorporated into, this Order that avoid or reduce the environmental effect identified in the FEIR to less than significant.

Facts Supporting the Findings:

· This Order requires minimization of hopper dredging inside San Francisco

Bay consistent with what the FEIR found would reduce impacts to less-than-significant levels. At a maximum, a hopper dredge would be used to maintain one federal channel inside the Bay and possibly urgent action removal of a hazardous shoal at Bulls Head Reach in the eastern approach to the Benicia- Martinez Bridge in Suisun Bay Channel if a mechanical dredge is not available (Provision 9).

· This Order requires compensatory mitigation for delta smelt entrainment in the form of mitigation credit purchase at a resource agency-approved habitat conservation bank. The amount of mitigation credit is calculated from an equation (3.0 million acre-feet/800 acres = volume dredged/X acres of mitigation habitat) that was developed by resource agencies to determine mitigation requirements for other projects with entrainment impacts resulting from pumping water (Provision 10).

· This Order requires implementation of specific avoidance, minimization, and mitigation measures, which combined with minimization of hopper dredge use, mitigates potential entrainment impacts to a less-than-significant level (Provision 11).

Impact 3.6-6: Potential Substantial Adverse Effects and Cumulative Impacts to Longfin Smelt from Entrainment Entrainment of longfin smelt could occurring during hopper dredging. They are not strong swimmers and are presumed susceptible to entrainment in the flow fields created around the intakes of hydraulic suction dredges. Longfin smelt have the potential to occur in any of the project areas in any season.

Findings: Changes or alterations have been required in, or incorporated into, this Order that avoid or reduce environmental effect identified in the FEIR to less than significant.

Facts Supporting the Findings:

· This Order requires minimization of hopper dredging inside San Francisco

Bay consistent with what the FEIR found would reduce impacts to less-than-significant levels. At a maximum, a hopper dredge would be used to maintain one federal channel inside the Bay and possibly urgent action removal of a hazardous shoal at Bulls Head…