R2-2015-0023_USACE_Nav_Dredging_WDR-WQC.PDF

CALIFORNIA REGIONAL WATER QUALITY CONTROL BOARD

SAN FRANCISCO BAY REGION

ORDER NO. R2-2015-0023

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, 2015 THROUGH 2019

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 a five-year period. The first two years of the project continue USACE’s current maintenance dredging program in terms of equipment type. Starting in 2017, 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 (Table 1), the maximum total dredging volume within San Francisco Bay is 12.4 million cubic yards (mcy) and the maximum total dredging volume in the San Francisco Main Ship Channel (MSC) west of the Golden Gate, outside San Francisco Bay is 2.5 mcy.

U. S. Army Corps of Engineers Maintenance Dredging 2015-2019 Order No. R2-2015-0023 Waste Discharge Requirements & Water Quality Certification

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 increase in sea level rise 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 increasing sea level and through 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 reduced in-Bay annual disposal goal of 1.25 mcy or less is described in the LTMS Management Plan (Management Plan), approved in July 2001 by the LTMS Executive Committee. 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 long-term goal. The transition period’s disposal volume limits were voluntary as long as in-Bay goals were met overall. Public assurance that in-Bay disposal would in fact decrease was provided by strict volume allocations to individual dredgers that could be triggered if goals were not met. 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 sites for smaller non-Corps projects. The 1.25 mcy annual in-Bay disposal goal allocates 250,000 cy/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 the 0.25 mcy “contingency volume” to be split between USACE and the medium-sized maritime industry dredgers. USACE’s average in-Bay disposal volume for 2015 through 2019 is expected to be within 0.625 – 0.750 mcy per year (50 to 60 percent of the 1.0 mcy in-Bay disposal goal plus the 0.25 mcy contingency volume it shares with other dredgers). The total not to exceed in-Bay disposal volume for this Order is 3.5 mcy (calculated as 0.7 mcy times five years). Further action by the Water Board will be required for in-Bay disposal in excess of this quantity.

Dredging Projects Summary

8. USACE’s maintenance dredging program provides for maintenance of 11 federal navigation channels in the San Francisco Bay, including six channels dredged annually and five channels with non-annual dredging cycles. These 11 channels have a combined surface area of 5,699 acres, which equates to 2.22 percent of the total surface area of San Francisco Bay. During each fiscal year from 2015 to 2019, USACE plans to dredge the seven 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), and San Francisco MSC. Other channels that USACE may dredge 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), the Brooklyn Basin (South Channel) portion of Oakland Harbor, San Bruno Channel, and San Leandro Marina (Jack D. Maltester) Channels. Each of these channels is either due or overdue for dredging.

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 - 11.

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 - 11 and shall not exceed the project depth, as shown in Table 1, 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 - 11.

Table 1 summarizes USACE’s 2015 - 2019 dredging program, including maximum 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.

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 creation, levee maintenance, or construction fill.

Existing beneficial reuse sites include: the Montezuma Wetlands Restoration Project (regulated by Water Board Order No. R2-2012-0089), the Cullinan Ranch Restoration Project (regulated by Water Board Order No. R2-2010-0108), and Winter Island levee maintenance (Figures 1, 5, 6, and 8). At their own discretion, dredging contractors or the project sponsors may propose to use other permitted upland 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 Demonstration Site (OBDS), which is encompassed by the future SF-17 placement site, in waters of the Pacific Ocean adjacent to the south-of-Sloat-Boulevard stretch of Ocean Beach (Figure 2). The OBDS 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. SF-17 is in the process of being formally designated as a disposal site under section 404 of the Clean Water Act.

Table 1. 2015 – 2019 Dredging Project Summary

Channel

Authorized or

Regulatory Depth (feet below MLLW)1 Dredge Type

Typical Dredging

Frequency (years)

Planning Volume per

Dredge Episode

(cy)

Water Board Preferred

Placement Site

Federal Standard

Placement Site2

Placement Site Alternate 13

Placement Site Alternate 23

Richmond Inner Harbor

Outer Harbor

41 Clamshell-Bucket annual 350,000 – 400,000

Habitat Restoration Beneficial Reuse

SF-DODS Upland Beneficial Reuse

Other In-Bay Site

45 Hopper*/Clamshell- Bucket annual 150,000 – 250,000

Habitat Restoration Beneficial Reuse

SF-11 Other In-Bay Site Upland Beneficial Reuse

Oakland Inner and Outer Harbor

Clamshell-Bucket annual 350,000 –

700,000 Habitat Restoration Beneficial Reuse

SF-DODS Upland Beneficial Reuse

In-Bay Site

Pinole Shoal Hopper*/Clamshell- Bucket annual 150,000 – 200,000

Habitat Restoration Beneficial Reuse

SF-10 Other In-Bay Site Upland Beneficial Reuse

Suisun Bay Channel and New York Slough4

35 Hopper/Clamshell- Bucket starting in annual 175,000 – 200,000

Habitat Restoration Beneficial Reuse

SF-16 Other In-Bay Site Upland Beneficial Reuse

Bulls Head5 Reach

Redwood City Harbor

30 Clamshell-Bucket (Harbor Channels) Hopper (San Bruno Channel)

1-2 300,000 – 600,000

Habitat Restoration Beneficial Reuse

SF-11 Other In-Bay Site Upland Beneficial Reuse except for San Bruno Channel;

SF-DODS for San Bruno Channel

Authorized or

Regulatory Depth (feet below MLLW)1 Dredge Type

Typical Dredging

Frequency (years)

Planning Volume per

Dredge

Placement Site

Federal Standard

Placement Site2

Placement Site Alternate 13

Placement Site Alternate 23

Petaluma River Channel (and Across the Flats^)

8 Cutterhead-Pipeline (River Channel) Clamshell-Bucket (Across the Flats)

4-7 150,000 Upland (Sponsor Provided) for the River Channel;

Habitat Restoration Beneficial Reuse for Across the Flats

Upland (Sponsor Provided) for the River Channel;

SF-10 for Across the Flats

Upland Beneficial Reuse

Other In-Bay Site

Napa River Channel^ Mare Island Strait Causeway to Asylum Slough

Cutterhead-Pipeline

6-10

140,000

Upland (Sponsor Provided) or Habitat Restoration Beneficial Reuse

Upland (Sponsor Provided)

Other Upland Site

SF-9 for downstream reach only Napa River

Channel^ Asylum Slough to Third Street

San Rafael Creek Channel - Across the Flats

Clamshell-Bucket

4-7

87,000 – 150,000

Habitat Restoration Beneficial Reuse

SF-11

Other In-Bay Site

Upland Beneficial Reuse San Rafael

Creek Channel – Inner Canal

San Leandro Marina (Jack D.

Maltester Channel)

8 Cutterhead-Pipeline 4-6 121,000 – 187,000

Habitat Restoration Beneficial Reuse

Upland (Sponsor Provided such as San Leandro

DMMS)

In-Bay Site Upland Beneficial Reuse

Authorized or

Regulatory Depth (feet below MLLW)1 Dredge Type

Typical Dredging

Frequency (years)

Planning Volume per

Dredge

Placement Site

Federal Standard

Placement Site2

Placement Site Alternate 13

Placement Site Alternate 23

San Francisco Bay 5-Year Maximum Dredge Volume: 12.4 mcy6

San Francisco Harbor – Main Ship Channel

55 Hopper annual 350,000 – 500,000

Ocean Beach Onshore

SF-8 SF-17 Ocean Beach Onshore

Main Ship Channel 5-Year Maximum Dredge Volume: 2.5 mcy Notes:

* Both Richmond Outer Harbor and Pinole Shoal could not be dredged with a hopper in the same year beginning in 2017 - see Provision 10.

^ For areas not dredged since 2000, the last dredging event is reported.

1 2-foot overdredge allowance 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 USACE cannot use placement sites until NEPA and/or CEQA environmental review and acquisition of required environmental approvals from resource and regulatory agencies is completed.

4 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.

5 Because of 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.

6 Assumes Redwood City Harbor is dredged annually and that the smaller, non-annual projects: Napa River Channel, Petaluma River Channel, San Rafael Creek Channel, and San Leandro

Marina Channel, are dredged once each during 2015-2019.

CEQA = California Environmental Quality Act cy = cubic yards mcy = million cubic yards NEPA = National Environmental Policy Act Ocean Beach Onshore = Onshore Ocean Beach placement site San Leandro DMMS = Upland San Leandro Dredged Material Management Site SF-8 = San Francisco Bar Channel Disposal Site (ocean site) SF-9 = Carquinez Strait placement site (in-Bay site) SF-10 = San Pablo Bay placement site (in-Bay site) SF-11 = Alcatraz Island placement site (in-Bay site) SF-16 = Suisun Bay placement site (in-Bay site) SF-17 = Ocean Beach placement site (near shore site, includes the Ocean Beach demonstration site) SF-DODS = San Francisco Deep Ocean Disposal Site (55 miles west of Golden Gate)

U. S. Army Corps of Engineers Maintenance Dredging 2015-2019 Order No. R2-2015-0023

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 upland/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

U. S. Army Corps of Engineers Maintenance Dredging 2015-2019 Order No. R2-2015-0023 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.

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.

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, Corps 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 (Corps Public Notice No. 93-3). Table 2, below, shows the monthly and annual

U. S. Army Corps of Engineers Maintenance Dredging 2015-2019 Order No. R2-2015-0023 maximum volume targets for all dredgers currently in effect for the in-Bay disposal sites.

This Order requires that USACE continue to enforce these maximum disposal volume targets in order to minimize water quality impacts associated with in-Bay disposal of dredged material.

Table 2. 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

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.

In the event that a project cannot be completed during the work window, USACE must consult with the appropriate federal resource agencies. The outcome of the individual consultation determines whether any additional dredging period for that project is appropriate and, if necessary, provides a “take authorization.”

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 as a result of 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

U. S. Army Corps of Engineers Maintenance Dredging 2015-2019 Order No. R2-2015-0023

Water Board, however, as explained further in Finding 18, must comply with CESA when issuing WDRs and Certification.

Since 2011, USFWS has required USACE to consult annually on impacts to delta smelt during dredging of Suisun Bay Channel and New York Slough because of documented occurrences of entrainment during monitoring of hopper dredge use in 2011. USACE will continue to complete annual consultations for hopper dredging of Suisun Bay Channel and New York Slough, as required by USFWS.

USACE and U.S. EPA have reinitiated formal federal Endangered Species Act consultation with NMFS to update its programmatic LTMS biological opinion to include green sturgeon, which was listed as threatened under the federal ESA in 2006. As stated in the October 14, 2014, Corps/U.S. EPA letter documenting agreement with NMFS’ Santa Rosa office staff on the updated LTMS program project description, the updated biological opinion will expand the salmonid work window to year-round if dredging is conducted with a clamshell dredge and dredged material is placed at a beneficial reuse site that NMFS agrees will provide aquatic habitat benefits for salmonids, such as a tidal wetlands restoration. 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) would require 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, or initiate individual project consultation and obtain written authorization from the resource agencies for work proposed outside of these windows.

17. Entrainment of Special-Status including Longfin Smelt and Delta Smelt: All forms of dredging have the potential to incidentally remove organisms from the environment with the dredged material, a process referred to as entrainment.

Organisms on the dredged material may be entrained in addition to organisms in the water column near the dredging apparatus. 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; 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 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.

U. S. Army Corps of Engineers Maintenance Dredging 2015-2019 Order No. R2-2015-0023

Entrainment Study: Over the past decade, 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 for longfin smelt, CDFW 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.

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 Certification. 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

U. S. Army Corps of Engineers Maintenance Dredging 2015-2019 Order No. R2-2015-0023 recommended reducing hopper dredging to a minimum in San Francisco Bay and implementing the avoidance, minimization, and mitigation measures listed below.

Fish & 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 10 and 11, will mitigate potential entrainment impacts to a less-than-significant level:

a. No dredging would 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. Implementation of a worker education program for listed fish species that could be adversely impacted by dredging. The program would 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. At the beginning and end of each hopper load, pump priming, drag head clearing, and suction of water would be conducted within three feet of the seafloor.

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

f. Completion of hydraulic hopper dredging in Suisun Bay between August 1 and September 30 to avoid impacts to spawning adult longfin and delta smelt.

g. Completion of hydraulic hopper dredging in Central Bay (i.e., Richmond Outer Harbor) between August 1 and November 30 to avoid impacts to young-of-the-year and spawning adult longfin smelt.

h. Maintaining contact of drag head, cutterheads, and pipeline intakes with the seafloor during suction dredging.

i. Keeping the drag head water intake doors closed to the maximum extent feasible in locations most vulnerable to entraining smelt. In circumstances when the doors need to be opened to alleviate clogging, the doors would be opened incrementally (i.e., the doors would 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

U. S. Army Corps of Engineers Maintenance Dredging 2015-2019 Order No. R2-2015-0023 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): On December 5, 2014, the Water

Board issued a draft Environmental Impact Report (EIR) for public review and filed a Notice of Completion with the State Clearinghouse (SCH). (Cal. Code Regs., tit. 14, § 15085.) The public comment period for the draft EIR (SCH No. 2013022056) was from December 5, 2014, to January 20, 2015. The Water Board received and evaluated comments on the draft EIR from public agencies and the other interested parties.

Responses to comments received during the comment period have been provided. The Water Board has considered, certified, and approved the final EIR (FEIR) pursuant to California Code of Regulations (CCR), title 14, sections 15090 - 15092.

The FEIR considers four alternatives:

No Project Alternative - Section 15126.6(e)(3)(A) of the CEQA Guidelines states that “when the project is the revision of an existing land use or regulatory plan, policy or ongoing operation, the no project alternative will be the continuation of the existing plan, policy or operation into the future.” Therefore, under the No Project Alternative, USACE would continue current 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 12.

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

12) 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 12 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.

U. S. Army Corps of Engineers Maintenance Dredging 2015-2019 Order No. R2-2015-0023

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.

Public Resources Code section 21002 declares the policy of the State that “agencies should not approve projects as proposed if there are feasible alternatives or feasible mitigation measures available which would substantially lessen the significant environmental effects of such projects.” (See also, Cal. Code Regs., tit. 14, §§ 15041 [“A lead agency for a project has authority to require feasible changes in any or all activities involved in the project in order to substantially lessen or avoid significant effects on the environment”] and 15042 [“A public agency may disapprove a project if necessary in order to avoid one or more significant effects on the environment would occur if the project were approved as proposed”].) Information in the record to date indicates that both Alternative 1 and Alternative 2 will substantially lessen the significant environmental effects of the Proposed Project. The FEIR concludes that both of these alternatives will reduce the impacts to less than significant. 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 12, and implementing the compensatory mitigation approach described above.

There is no information in the record to date that indicates either Alternative 1 or Alternative 2 is infeasible. For this reason, this Order permits either Alternative 1 or 2.

This Order will not have a significant impact on the environment except as specified below. For the following impacts, this Order has eliminated or substantially lessened all significant effects on the environment where feasible. Pursuant to CCR, title 14, sections 15091 and 15093, the Water Board makes the following CEQA Findings and Statement of Overriding Considerations in conjunction with the approval of this Order:

CEQA Findings

Impact 3.6-4: Potential Adverse Effects from Entrainment on Special-Status or Commercially and Recreationally Important Marine Species, Not Including Delta Smelt and Longfin Smelt

During all forms of dredging, organisms on the dredged material may be entrained in addition to organisms in the water column near the dredging apparatus.

Findings: With implementation of the LTMS work windows as required by Provision 13 and other avoidance, minimization, and mitigation measures intended to reduce the potential for entrainment required by Provision 12, effects to special-status and commercially important species, not including delta smelt and longfin smelt, would not be significant.

Impact 3.6-5: Potential Substantial Adverse Effects and Cumulative Impacts to Delta Smelt from Entrainment

U. S. Army Corps of Engineers Maintenance Dredging 2015-2019 Order No. R2-2015-0023

Delta smelt 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 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 substantially lessen the significant environmental effect as identified in the

FEIR.

Facts Supporting the Findings:

This Order requires implementation of reduced hopper dredge use inside San Francisco Bay starting in 2017. 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 10).

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 as a result of pumping water (Provision 11).

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 12).

Impact 3.6-6: Potential Substantial Adverse Effects and Cumulative Impacts to Longfin Smelt from Entrainment

Longfin 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.

Findings: Changes or alterations have been required in, or incorporated into, this Order that avoid or substantially lessen the significant environmental effect as identified in the

FEIR.

Facts Supporting the Findings:

This Order requires implementation of reduced hopper dredge use inside San Francisco Bay starting in 2017. 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 10).

This Order requires compensatory mitigation for longfin 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

U. S. Army Corps of Engineers Maintenance Dredging 2015-2019 Order No. R2-2015-0023 developed by resource agencies to determine mitigation requirements for other projects with entrainment impacts as a result of pumping water (Provision 11).

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 12).

Impacts 3.7-1, 3.7-2, and 3.7-3: Disturbance of Archaeological Resources, Human Remains, and Paleontological Resources

Although unlikely, given the repeated dredging and dredged material placement activities that have historically occurred at the federal navigation channels and existing placement sites, there remains the potential that archaeological materials, human remains, or paleontological materials could be inadvertently uncovered by project activities.

Findings: With implementation of the mitigation measures required by Provision 22, impacts to cultural and paleontological resources would be less than significant. These measures consist of immediate suspension of dredging upon discovery of a resource and consultation with a qualified expert for the particular resource discovered (e.g., archaeologist, paleontologist, local coroner, Native American Heritage Commission).

Statement of Overriding Considerations The Water Board recognizes that prior to implementation of reduced hopper dredge use in 2017, the project could have significant, unavoidable impacts to biological resources as identified in the FEIR. The Water Board has considered and balanced the economic, legal, social, technological, and other benefits of this Order. The Water Board finds that the unavoidable adverse impacts are acceptable due to overriding concerns. Specifically, the following benefits outweigh the adverse impacts:

The San Francisco Bay/Delta Estuary is one of the critical maritime thoroughfares in the nation, supporting international trade, commercial and recreational fishing, and recreation. Maintenance dredging is necessary to provide a safe, reliable, and efficient waterborne transportation system (federal channels, harbors, and waterways) for the movement of commerce, national security, and recreation.

Maintaining the federal channels to their regulatory depths is critical to the region’s maritime trade and to the regional and national economies.

In accordance with Title 14 of CCR section…