ENV Attachment 1 for reference.pdf

United States Department of the Interior

In reply refer to:

08FBDT00-2017-F-0098

Mark T. Zirninske

FISH AND WILDLIFE SERVICE

San Francisco Bay-Delta Fish and Wildlife Office

650 Capitol Mall, Suite 8-300 Sacramento, California 95814

Chief, Environmental Resources Branch Department of the Army Corps of Engineers, Sacramento District 1325 J Street Sacramento, CA 95814-2922

U.S.

FISH & WlLDLJFE

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Subject: Formal Consultatior.. on the Stockton Deep Water Shipping Channel Dredging and Bank Stabilization Project, Sacramento, Contra Costa, and San Joaquin Counties, California

Dear Mr. Zirninske:

This letter is in response to the U.S. Army Corps of Engineers' (Corps) February 9, 2017, request for formal consultation with the U.S. Fish and Wildlife Service (Service) on the proposed Stockton Deep Water Shipping Channel (SDWSC) Dredging and Bank Stabilization Project (project), in Sacramento, Contra Costa, and San Joaquin Counties. The proposed project is within and along the Deep Water Shipping Channel in the San Joaquir.. River. The Corps has determined that the project may affect, and is likely to adversely affect the threatened giant garter snake (Thamnophis gigas; GGS), the threatened delta smelt (Hypomesus transpacificus) and its critical habitat. The Corps has also determined that the project may affect, but is not likely to adversely affect the threatened valley elderberry longhorn beetle (Desmocerus californicus dimorphus; VELB). The Corps has requested a multiple-year biological opinion (BO) that incorporates additional avoidance and minimization measures associated with extremely low delta smelt abundance and includes flexibility for changes in baseline conditions. This response is in accordance with section 7 of the Endangered Species Act of 1973, as amended ( 16 U.S. C.

1531 et seq.) (Act).

This response is based upon information from: (1) the undated Stockton Deep Water Ship Channel Maintenance Dredging and Bank Protection Project, California Biological Assessment from the Corps for the 2017 dredging season; (2) the Corps' February 9, 2017, request for reinitiation of consultation for this project; (3) the November 2016 - February 2017, meetings, emails, and telephone communications between the Service and the Corps about the project description; (4) the Service's August 12, 2016 BO on the 2016 Sacramento and Stockton Deep Water Shipping Channels Dredging and Bank Stabilization Project (S~rvice File No. 08FBDT00- 2016-F-0098); and (5) other information available to the Service.

Mr. Mark T. Ziminske

The Corps proposes to continue conducting pre-dredging surveys on the proposed Dredging Material Placement Sites (DMPSs) to identify any elderberry shrubs (Sambucus sp.),which are the sole host plant for the VELB, and completely avoid them by maintaining a 100-foot (ft) or greater buffer from the shrub. The Service concurs with the determination that the project may affect, but is not likely to adversely affect the VELB based on the Corps' proposal to avoid impacts to the VELB' s host plant.

This document hereby represents the Service's biological opinion on the effects of the 5-year implementation of the SDWSC project on the GGS, the delta smelt, and the delta smelt's critical habitat.

August 12, 2016

November 2016- February 2017

CONSULTATION IDSTORY

The Service issued its BO for the 2016 Sacramento River Deep Water Shipping Channel (SRDWSC) and SDWSC Operations and Maintenance Dredge Project.

The Service provided the Corps with technical assistance during meetings and through email communications on the development of the 5-year project description and separation of the SRDWSC and SDWSC into two consultations.

BIOLOGICAL OPINION

Description of the Proposed Action

Stockton Deep Water Shipping Channel

The SDWSC extends from the upstream end of New York Slough to the City of Stockton within the San Joaquin River. The SDWSC varies in width from 200 to 600 ft, except in the turning basin at the Port of Stockton where it is 970 ft wide. The 36.4 miles of waterway, from river mile (RM) 3.8 to RM 39.2 and RM 40.1toRM41.1 have a design depth of 35 ft below mean lower low water (MLL W). The reach from RM 40. l to RM 41.1 has a design depth of 40 ft and is designed to function as a sediment trap.

The SDWSC proposes to utilizes ten different DMPSs located at the Antioch Dunes, Bradford Island, two sites on Sherman Island (Scour Pond and McCormick Pit), two sites on Twitchell Island (Twitchell North and Twitchell South), one site on Mandeville Island, two sites on Roberts Island (Roberts Island I and Roberts Island II), and one site on Rough and Ready Island.

SDWSCDMPSs

There are currently ten DMPSs for the SDWSC as shown in Table 1 and discussed in detail below. Table 2 shows the total site acreage dredged in the channel around each DMPS.

Table 1. Stockton Deep Water Ship Channel DMPSs

Placement Site

Antioch Dunes Class I Site

Sherman Island Scour Pond Class f Site

Sherman Island McCormick Pit Class I Site

Bradford Island Class II Site

Twitchell North

Twitchell South

Mandeville Island

Method of Return Water and site specifications

Gravity. Water leaves through gravity drain into the San Joaquin river.

Ponding time: 30 hours (hrs) Ponding area: 10 acres (ac) Ponding vol: 50,000 cubic yards (cy) Pump. Water leaves site by gravity into agriculture ditch with pump out by Reclamation District (RD).

Ponding time: 325 hrs Ponding area: 60 ac Ponding vol: 300,000 cy Pump. Water leaves site by gravity into agriculture ditch with pump out by RD.

Ponding time: 60 hrs Ponding area: 25 ac Ponding vol: 110,000 cy

Pump. Water leaves site by gravity into agriculture ditch which Contractor pumps out.

Ponding time: 310 hrs Ponding area: 60 ac Ponding vol: 290,000 cy

Pump. Water leaves site by gravity into agriculture canal, then to San Joaquin River via pump.

Ponding time: 65 hrs Ponding area: 3 8 ac Ponding vol: 120,000 cy

Pump. Water leaves site by gravity into agriculture canal, then to San Joaquin River via pump.

Ponding time: 56 hrs Ponding area: 32 ac Ponding vol: 103,000 cy

Water leaves site by gravity into agriculture canal.

Ponding time: 3 8 hrs Ponding area: 22 ac Ponding vol: 71,000 cy

Point of Contact

Port of Stockton

Port of Stockton/

RD 341

Port of Stockton I

RD341

Port of Stockton

Port of Stockton

Port of Stockton

Port of Stockton

Special Requirements

National Wildlife Refuge and habitat restoration site.

Site underlain by peat; No placement or decant water in adjacent pond.

Site underlain by peat.

Only access to island is by boat;

Agriculture ditch pumped out by RD-2059/ Port owned pumps Benn Construction and dredged material should avoid irrigation/ drainage canal.

Dredge pipeline may span the canal Irrigation/ drainage canal regulated by the Corps, Central Valley Regional Water Quality Control Board, and California Dept. of Fish and Wildlife.

Landing Point; Line Pump Allowance

Station 314+00 Allowance 2,300 ft

Station 423+00;

Allowance = 900 ft

Station 564+00;

Allowance = 3,700 ft

Station 740+00;

Allowance = 500 ft

These are newly proposed sites. No data available

These are newly proposed sites. No data available

These are newly proposed sites. No data available

Mr. Mark T. Ziminske 4

Placement Site Method of Return Water and Point of Special Landing Point; Line site specifications Contact Requirements Pump Allowance

Roberts Island Pump. Water leaves site by Port of May be under Station 1618+00;

II Class I Site gravity into agriculture ditch Stockton cultivation Allowance = 600 ft which Contractor pumps out.

Ponding time: 3 10 hrs Ponding area: 50 ac Station 1840+00;

Ponding vol: 240,000 cy Allowance = 600 ft

Roberts Island I Pump. Water leaves site by Port of May be under Station 1895+00;

Class I Site gravity into agriculture ditch Stockton cultivation Allowance = 300 ft which Contractor pumps out.

Ponding time: 600 hrs Ponding area: 110 ac Station 1975+00;

Ponding vol: 530,000 cy Allowance = 300 ft

Rough and Pump. Water leaves site by Port of Station 2 I 05+o0 Ready Island gravity into agriculture ditch Stockton Allowance= 2,750 ft which Contractor pumps out.

Ponding time: 290 hrs Ponding area: 46 ac Ponding vol: 250,000 cy

T bl 2 T t I £ td d d£ .a e o a acre ee re 1ee or eac hDMPS b tw e een 2000 d 2013 an Stockton DWSC (Acre Feet Dredged)

2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 Total

Antioch 25 25 Dunes Scour Pond 18 49 3 30 30 6 136

McCormick 3 19 22 8 25 8 84 Pit Bradford 9 25 18 20 12 13 95 Island Roberts l 19 45 119 90 115 118 24 118 66 7 15

Roberts II 27 38 3 1 18 30 59 1 7 210

Rough and Ready Twitchell These are newly proposed DMPSs, so no data is available. Estimated maximum volumes for each site are 38 acre feet North for Twitchell North, 32 acres for Twitchell South, 22 acres for Mandeville Island.

Twitchell South Mandeville

Avg 44 38 30 35 26 50 69 54 49 51 15 45 66 13

Total 177 38 60 141 77 100 138 109 195 202 76 179 66 38

Antioch Dunes National Wildlife Refuge (ADNWR)

The ADNWR is an approximate 55-acre refuge managed by the Service that consists of two parcels separated by the Georgia-Pacific Gypsum Plant and a Pacific Gas and Electric utility easement. The 41-acre western parcel (Stamm Unit) is the only parcel proposed to receive dredge sediment for this project. As part of Comprehensive Conservation Plan (CCP) for the ADNWR, dune restoration is one of the primary objectives for habitat restoration. Beginning in 1991 , the Service has imported sand to the ADNWR in order to create additional habitat for listed species that occur on the refuge. The CCP specifies identifying potential sources of clean sand, specifically around the SDWSC. In 2013, the Port of Stockton and the Service partnered

Mr. Mark T. Ziminske 5 with the Corps to begin restoration efforts using dredged material (Service File No. 08ESMF00- 2013-I-0500). Continued use of this DMPS as a site for beneficial reuse of dredged material will eventually allow restructuring of the sand dunes and possibly recreating the natural function and habitat value of the ADNWR. This site was used as a DMPS in 2013 and 2015.

Sherman Island Scour Pond

This DMPS is a 125-acre site located on Sherman Island, just west of the Antioch Bridge, on the Antioch North United States Geological Survey quadrangle map in Sacramento County. Some areas are bermed, while others would receive berms prior to use as a DMPS. The existing berm is located outside the marsh fringe around Scour Pond and is currently pastureland. A 200-foot buffer would be maintained around Scour Pond. No decant water or dredged materials would be placed or allowed to drain into the scour pond portion of the site. The California Department of Water Resources (DWR) and RD 341 maintain the Scour Pond site. This site has been used as a DMPS in 2007, 2008, 2009, 2010, 2011, and 2013.

McCormick Pit

This DMPS is a 26-acre site located on Sherman Island, east of the Antioch Bridge along the SDWSC, on the Jersey Island USGS quadrangle map in Sacramento County. The site is bermed and contains sand material from past maintenance dredging. There is an emerging freshwater marsh located on a portion of this site as a result of past placement of dredged materials .

Dredged material would be placed in non-wetland areas of this site. The water that caiTies the dredged material would drain through the wetland areas into an agricultural drainage canal on Sherman Island which is pumped back to the river by RD 341. DWR and RD 341 maintain the McCormick Pit site. This site has been used as a DMPS in 2002, 2008, 2009, 2010, 2011, 2013, 2014, and 2015.

Bradford Island

This DMPS is a 110-acre site located on the southwestern portion of Bradford Island, at the confluence of the San Joaquin and False Rivers, on the Jersey Island USGS quadrangle map in Contra Costa County. The site is bermed and is currently irrigated pastureland. There are drainage ditches that transect a portion of the site and there is evidence of subsidence. There is some ponded water onsite, which would be avoided during dredged material placement. The water that carries the dredged material may drain into the ponded areas and eventually recede via a culvert into the river. This site, contains a landing allowance of 500 ft, and has been used in past maintenance dredging practices. The Port of Stockton and RD 2059 maintain the Bradford Island site. This site has been used as a DMPS in 2000, 2003, 2006, 2010, and 2015.

Twitchell North and South

The Twitchell Island North DMPS is a 38-acre site located at the northeastern side of Twitchell Island, on the Bouldin Island USGS quadrangle map in Sacramento County, and consists of an agricultural field and the associated irrigation/drainage canals. The existing levee at the Twitchell North site runs 1,460 linear feet on the east side of the site. Lands to the south and southwest are managed for waterfowl habitat and include freshwater emergent wetlands with open water. East of the site is Seven Mile Slough, which also includes open water and freshwater emergent marsh.

The Twitchell Island South DMPS is a 32-acre site located on the southeastern side of Twitchell Island and consists of an alfalfa field. The existing levee bordering Twitchell South runs 54,200 linear feet along the east and south sides of the site. Adjacent land uses to the north and west consists of lands managed for waterfowl habitat and include freshwater emergent wetlands.

These are new DMPSs. The proposed action involves construction activities to prepare the new DMPSs for use, placing dredge slurry in the site, and maintaining the sites between dredging episodes in the future as needed. To prepare the site for dredged material placement, containment berms would be constructed around the perimeter of the proposed placement area at each site.

The containment berms would be a maximum of 8 ft high. Due to existing site topography, the berm heights (from the bottom to top) would vary, but the elevation of the top of the berm would remain consistent in all areas. The berm would have a slope of2.5:1 , and the top of the berm would be 12 ft wide to allow for truck access. Soils existing on site would be graded to form the berms. Interior dikes may be installed within the footprints of the DMPS. Berm construction activities would occur over approximately 6 weeks for each site. Construction would occur up to 7 days per week between the hours of 6 a.m. to 7 p.m. Construction equipment would include scrapers, a bulldozer, a water truck, and a compactor.

Mandeville Island

The Port of Stockton also proposes to add a new DMPS on Mandeville. The 22-acre site is located on the northeastern corner of Mandeville Island, adjacent to the San Joaquin River. The existing levee at the Mandeville site runs 2,200 linear feet along its eastern side. To prepare the site for dredged material placement, containment berms would be constructed around the perimeter of the proposed placement area at each site. The containment berms would be a maximum of 8 ft high. Due to existing site topography, the berm heights (from the bottom to top) would vary, but the elevation of the top of the berm would remain consistent in all areas. The berm would have a slope of2.5 :1, and the top of the berm would be 12 ft wide to allow for truck access. Soils existing on site would be graded to form the berms. Interior dikes may be installed within the footprints of the DMPS. Berm construction activities would occur over approximately 6 weeks for each site. Construction would occur up to 7 days per week between the hours of 6 a.m. to 7 p.m. Construction equipment would include scrapers, a bulldozer, a water truck, and a compactor.

Roberts Island II

This DMPS is a 220-acre site located on Roberts Island, between the outlet of Black Slough and the Windmill Cove marina in San Joaquin County. The site is bermed and has been used as a DMPS in the past. The majority of the site is clay with little vegetation. The landing allowance is 600 ft and the site is maintained by the Port of Stockton. This site has been used as a DMPS in 2000,2001,2003,2004,2005,2009,2010,2011,and2015.

Roberts Island I

This DMPS is a 250-acre site located on Roberts Island, northwest of the West Complex, Port of Stockton, and adjacent to House Road. This site has a matrix of bare sand and short herbaceous vegetation; it is bermed and has been used as a DMPS in the past. The landing allowance is 300 ft and the Port of Stockton maintains the site. This site has been used as a DMPS in 2000, 2003, 2006, 2007, 2008, 2009, 2010, 2011, and 2012.

Rough and Ready Island

The Rough and Ready Island DMPS is an approximately 50-acre upland area located in the southeast quadrant of Rough and Ready Island to the north of Burns Cutoff. It has been in use since 2013, and is owned and operated by the Port of Stockton.

Purpose and Need for Maintenance Dredging and Bank Stabilization

The Corps proposes to continue to perform routine maintenance dredging and bank protection on the SDWSC under Indefinite Delivery/Indefinite Quantity contracts. The project includes work using a hydraulic pipeline dredge and clamshell crane for rock placement. The dredged material would be deposited at previously authorized DMPSs. Dredge slurry would be routed to the DMPSs via pipelines. DMPSs would be diked in order to allow dredge slurry to settle and consolidate. Decant water would then be discharged back into the SDWSC respectively, from some DMPSs, as determined during annual coordination. Dredged spoils would be allowed to dry in the DMPSs. The bank protection rock placement may be placed at any site that previously contained bank protection work, and where there is a need for additional rock due to bank erosion following specific work-windows to minimize effects to federally listed species and critical habitats.

Shoaling must be removed to maintain adequate channel depth for commercial shipping traffic that uses the navigation channels. Failure to perform maintenance dredging would result in unsafe conditions and a restriction on access to the Port of Stockton from the San Francisco Bay.

Failing to dredge the channels poses both a substantial risk to human safety as well as an economic harm to the Port and the commercial activities that use the Port's facilities.

Maintenance bank protection work is needed to maintain the integrity of existing bank protection placed to prevent erosion of the ship channel banks. Such bank erosion usually occurs due to wave action caused by ship traffic. Maintenance bank stabilization, in the form of rock replenishment, would stabilize the channel alignment and preserve the general uniformity of the bank lines. The channel banks protect ship channel traffic from adverse crosscurrents during the occurrence of flood flows.

The Corps proposes to conduct its annual operations and maintenance dredging in the SDWSC during the 5-year term beginning approximately August 1, 2017, and finishing approximately October 31, 2022. Prior to each dredging season, the Corps will coordinate with the Service. This would include documentation of exact reaches of the SDWSC to be dredged, schedule for that dredging year, and which DMPS would likely be used. Separate documentation will be provided to the Service if there are changes to DMPS boundaries, location, or function.

All sites along the SDWSC would be dredged to maintain the current navigational depth:

• The lower portion of the channel would be maintained at a depth of 30 ft below MLL W

• The upper portion of the channel would be maintained at a depth of 35 ft below MLLW

• An over depth of 1 or 2 ft is also anticipated for all sites. These depths maintain safe conditions for ships using the channels while not increasing the quantity or size of commercial navigation traffic.

Mr. Mark T. Ziminske 8

The project includes the use of a hydraulic cutter head suction dredge for dredging. Dredged materials would be deposited at previously authorized DMPS. Dredge slurry would be routed to the DMPS via pipelines. DMPS would be diked, and dredge slurry would be allowed to settle and consolidate. Depending on the size of the DMPS and the amount of material being dredged, the decant water could be released from the DMPS into the river. Effluent discharge from all DMPSs are allowed only with prior approval from the Central Valley Regional Water Quality Control Board (CVRWQCB) through the 401 Water Quality Certification. Dredged spoils would be allowed to dry and the land returned to prior uses.

The quantity of material to be dredged is not expected to exceed 500,000 cy, barring monumental flood events. The hydraulic dredge is expected to operate 24 hours a day, 7 days a week. When the dredge is positioned in a location where shoaling is to be removed, the dredge anchors itself by alternatively planting one or two "spuds," or vertical poles, into the bottom sediment. The dredge rotates around whichever of the two spuds is planted by pulling on "swing" anchors, alternately raising and planting the spud as the dredge "walks" forward. The hydraulic pipeline cutterhead dredge is equipped with a rotating cutterhead (excavator) surrounding the intake of the suction line. At that point, the solids and a large volume of the surrounding water are passed through the dredge centrifugal pump to the discharge pipeline as slurry. The slurry typically has a solids content of 10 to 20 percent by weight.

Dredging activities would be limited to depths greater than 25 ft, and the cutterhead would be kept within 3 ft of the channel bottom while drawing in water. The cutter head is mounted on a "ladder" that is free to pivot in the vertical plane and is rotated down to various depths. The ladder would be mounted on a floating dredge that swings left and right while proceeding along the channel. The dredge could be self-propelled or transported to the area by a tugboat.

Typically, the dredge is tended by two tenders that pick up and place the swing anchors as the dredge progresses and can move the dredge short distances. There are also two outboard engine powered skiffs that transport crews and conduct the water sampling upstream and downstream of the dredge.

The discharge pipeline would run from the dredge in the channel, across the bank, and onto the relevant DMPS. At all DMPSs, a nominal area of outboard levee area would be temporarily disturbed during the positioning of the slurry pipe. To minimize disturbance, a survey would be taken of the area immediately prior to pipe placement and upon completion of the dredging operation, any disturbed banks would be restored to pre-project conditions. Coordination will occur to ensure all discharge piping will be placed to avoid or minimize effects to listed species or habitats.

The pipeline would be made of durable plastic and would alternately float or sink depending on the specific gravity of the material it contains. The pipeline would float approximately 2 inches above the water surface when filled with water or air, and would rest on the channel bottom while containing dredged material and water. The dredge contractor would determine the best route for the pipeline (per the disposal plan) in conjunction with a qualified biologist to avoid listed species or habitat. The pipeline would be marked by buoys and/or high visibility paint to warn boaters of its presence. Additional safety measures may include signs, flaggers, and/or other measures as required.

Bank Stabilization

Suitable rock protection would be placed at eroded sites along the SDWSC. Where scour, wash, settlement, or failure of a portion of the original rock protection has been noted, or where inspection indicates that such damage may result during the next flood or high water period, the scour or wash would be filled with earth free from brush, roots, sod, or other unsuitable material and additional stone would be placed upon the earth fill. This maintenance bank stabilization would bring the rock protection to its original section, using rock fill, embankment, filter, and quarry rock. The rock used would, as much as possible, be similar to the kind and gradation as originally used, as described in the 1980 and 1986 Environmental Impact Statement documents.

Along river bank reaches of the SDWSC, where filter material was originally placed or where it may be required, maintenance repair of rock protection would include the placement of a properly graded filter layer under the rock protection. In the event an inspection reveals that due to scour, settlement or other causes, rock protection on the bank is required beyond the limits of the original construction or in reaches of the bank not originally provided with such protection, the Corps would provide additional sloping of the bank and placement of rock protection, as needed, to protect completed works and will reinitiate consultation as appropriate.

Activities in shallow water habitats would be avoided to the fullest extent possible. However, proposed maintenance bank stabilization work may involve some shallow water areas. This maintenance bank protection work is located along both banks of the manmade portion of the SDWSC at various locations. Rock may be placed at any site that previously contained bank protection work, and where there is a need for additional rock due to bank erosion. Rock may be placed at any site that previously contained bank protection work, and where there is a need for additional rock due to bank erosion. Depending on conditions at each site, rock may be placed using barges or from a levee using ground equipment. The Corps proposes to conduct bank stabilization between June 15 and November 30.

Project Avoidance and Minimization Measures

The Corps proposes the following avoidance and minimization measures to reduce adverse project effects to delta smelt and its critical habitat, and GGS. These avoidance and minimization measures would be followed by the Corps and their dredging contractor(s) during all maintenance dredging work. These measures would either be written by the Corps into the dredging contract(s) as a requirement of the contractor to adhere to during dredge-work, or would be taken into account when the Corps issues task orders under the dredging contract, as appropriate:

1. Maintenance dredging will be conducted between August 1 through October 31 work window for the SDWSC.

2. Dredging at depths less than 25 ft will be avoided to the fullest extent possible.

3. Cutter heads will not be operated more than 3 ft above the channel bottom.

4. Suction dredging will not be operated as the dredge head is deployed and retrieved through the water column.

Mr. Mark T. Ziminske 10

5. The suction head will be maintained at a constant elevation near the channel bed when dredging, to reduce the field of influence where fish may be entrained into the dredge pipe. Rather than dredging the entirety of the channel and swinging the suction through a "water hole" mid-channel, dredging will occur just along the channel edges where there is adequate material, thus minimizing exposure to open water areas where entrainment would be more likely.

6. A drag beam or similar device will not be used to "knock down" ridges or high spots in the channel bottom.

7. Bank stabilization work in shallow water habitat will be avoided to the maximum extent possible.

8. A fish entrainment monitoring program has been implemented over the lifetime of the previous 10-year programmatic biological opinion in order to quantify the level of incidental take of special status species from the dredging operations, assess the effects of maintenance dredging and dredge material placement on water quality, and provide feedback to the Corps to lessen potential environmental effects of the long-term dredging activities. This fish monitoring program has been ongoing since 2006 and has been utilizing adaptive management practices in order to improve the effectiveness of the monitoring. Part of the adaptive management has included the design of a fish entrainment device to allow more effective monitoring and further reduce adverse effects. Entrainment monitoring will be implemented during each dredging season.

9. The Corps will coordinate their annual project dredging schedule and plans with Service, National Marine Fisheries Service (NMFS), and California Department of Fish and Wildlife (CDFW) before the beginning of each dredging season with the intent of reducing and avoiding any adverse project effects to listed species and designated critical habitats. In addition, a biological monitor will conduct pre-dredging, aquatic and/or terrestrial pre-construction surveys for VELB, and GGS, prior to all maintenance dredging.

10. Since maintenance dredging and bank protection work near potential GGS habitat(s) may occur up to November 30, beyond the GGS October 1 work-window limit, the Corps will notify the Service of potential work that may affect GGS. A Service approved biological monitor will survey the bermed area(s) before dredging to ensure that no activities will occur within 200 ft of suitable GGS habitat including suitable aestivation habitats such as rock outcroppings or small animal burrows. Dredging personnel will participate in a Service-approved worker training briefing to learn about the presence of GGS and its habitat. The workers will also be informed of the consequences of unlawful take of the animal or destruction of its habitat. If an individual GGS is encountered, activities will cease and any sightings would be immediately reported to the Service.

11. In order to reduce potential impacts to GGS, when near sensitive habitat, movement of heavy equipment would be confined to existing levee top roads and designated construction access corridors that avoid suitable GGS habitat (wetlands and irrigation ditches). A speed limit of 10 miles per hour will be established on levee roads or other areas near potential GGS habitat that do not have a posted speed limit. Contractors will be instructed to be aware of their surroundings while driving and snakes on the road will be avoided.

12. All decant water will be monitored for CVRWQCB constituents of concern and physical parameters. Management practices will include placing flash boards at the spillway of DMPS to increase the retention time, using interior dikes within the DMPS to increase the hydraulic efficiency of the DMPS, and varying the dredge production rates . Decant water will only be discharged to the river if it meets all of the water quality standards stated in the CVRWQCB Waste Discharge Requirements General Order. If the water does not meet the standards, then it will be retained on the relevant DMPS until further analyses reveal such compliance. The effluent will not exceed Water Quality Objectives or criteria for any constituent that is on the Section 303(d) list.

13. The effects to water quality will further be minimized by not allowing the release of oils, grease, waxes, or other materials that could form a visible film or coating on the water surface or on the stream bottom or creating a nuisance or adversely affecting beneficial uses. Any spills of hazardous materials will be cleaned up immediately and reported in compliance reports.

14. The contractor will be responsible for providing erosion and sediment control measures in accordance with Federal, State, and local laws and regulations to ensure compliance with water quality standards. This will be accomplished by installing temporary and permanent erosion and sediment control best management practices. These may include, but are not limited to, vegetation cover, stream bank stabilization, slope stabilization, silt fences, construction of terraces, interceptor channels, sediment traps, inlet and outfall protection, diversion channels, and sedimentation basins. Any temporary measures would be removed after the area has been stabilized.

15. Upon completion of the dredging operation, any disturbed banks will be restored to pre project conditions.

Action Area

The action area is defined in 50 CFR § 402.02, as "all areas to be affected directly or indirectly by the Federal action and not merely the immediate area involved in the action." For the proposed project, the action area encompasses portions of the SDWSC, with their associated river banks in the San Joaquin River, as well the ten DMPSs within the legal California Delta (See Attachments for maps) . This constitutes approximately 443 total channel acres (geospatial) of the dredging footprint area. This is based on the total of the highest acre feet dredged for each of the seven historically utilized DMPSs and the estimated volumes for the three newly proposed DMPSs (See Table 2). There are approximately 453 terrestrial acres for the ten DMPSs. This is based on the total ponding area of the ten DMPSs (See Table 1).

Mr. Mark T. Ziminske 12

Status of the Species

Delta Smelt

Legal Status

The Service proposed to list the delta smelt (Hypomesus transpacificus) as threatened with proposed critical habitat on October 3, 1991 (Service 1991 ). The Service listed the delta smelt as threatened on March 5, 1993 (Service 1993), and designated critical habitat for the species on December 19, 1994 (Service 1994). The delta smelt was one of eight fish species addressed in the Recovery Plan for the Sacramento-San Joaquin Delta Native Fishes (Service 1996), and a revision addressing delta smelt is currently underway. A 5-year status review of the delta smelt was completed on March 31, 2004 (Service 2004). The 2004 review concluded that delta smelt remained a threatened species. A subsequent 5-year status review recommended uplisting delta smelt from tlu·eatened to endangered (Service 2010a). A 12-month finding on a petition to reclassify the delta smelt as an endangered species was completed on April 7, 2010 (Service 2010b). After reviewing all available scientific and commercial information, the Service determined that re-classifying the delta smelt from a threatened to an endangered species was warranted but precluded by other higher priority listing actions (Service 201 Oc). The Service annually reviews the status and uplisting recommendation for delta smelt during its Candidate Notice of Review (CNOR) process. Each year, the CNOR has recommended the uplisting from threatened to endangered. Electronic copies of these documents are available at http://ecos.fws.gov/docs/five_year_review/doc3570.pdf and http://www.gpo.gov/fdsys/pkg/FR- 2013- l 1-22/pdf/2013-27391.pdf (Service 2010a; Service 2010b).

Description and Life Cycle

The delta smelt is a small fish of the family Osmeridae. It is endemic to the San Francisco Bay Delta where it primarily occupies open-water habitats in Suisun Bay and marsh and the Sacramento-San Joaquin Delta. The delta smelt is primarily an annual species, meaning that it completes its life cycle in one year which typically occurs from April to the following April plus or minus one or two months. In captivity delta smelt can survive to spawn at two years of age (Lindberg et al. 2013), but this appears to be rare in the wild (Bennett 2005). Very few individuals reach lengths over 3.5 inches (90 mm).

Population Numbers

The spawning stock of delta smelt in Water Year (WY) 2017 appears to be at its second lowest abundance on record, the lowest having been recorded during WY 2016 (Table 3). The 2017 Fall Midwater Trawl (FMWT) Index was 8, the second lowest on record. The CDFW Spring Kodiak Trawl (SKT) monitors the adult spawning stock of delta smelt and serves as an indication for the relative number and distribution of spawners in the system. The 2017 SKT Abundance Index is 3.8, the second lowest on record. The Service calculated an absolute abundance estimate1 for adult delta spawners in WY 2017, using January and February SKT data. This absolute abundance estimate is also the second lowest on record (Table 3). The population size of adult

I The Service completed a revised adult delta smelt abundance estimation procedure based on CDFW's SKT data for January and February (see Table 2.). This procedure has recently been updated from that used in 2016. While these estimates likely represent a minimum population size due to the method reliance on survey data, this is our current best estimate of the annual population size.

Mr. Mark T. Ziminske 13 delta smelt January through February 2017 was estimated to be between 22,000 and 92,000 fish with a point estimate of 47,786. The January through February, 2016 point estimates were the lowest values since 2002 and suggested delta smelt experienced increased mortality during the extreme drought conditions occurring during 2013-2015. While 2017 estimates likely represent an increase in recruitment and survival from the prior year, the continued low parental stock of delta smelt relative to historical numbers suggests the population will continue to be vulnerable to stochastic events and operational changes until successive years of increased population growth result in a substantial increase in abundance.

Table 3. Three indicators of adult delta smelt status for WYs 2002-2017. Column 2 is the CDFW FMT Index by WY (i.e., the indices for calendar years 2001-2016). Column 3 is the CDFW SKT Index. Column 4 is an estimate of adult delta smelt abundance during January and February that h S . 1 ul f h SKT t e erv1ce ca c ates rom t e survey.

FMWT

SKT Index

January and February SKT Abundance WY Index

(unitless) Estimate (number of delta smelt)

(unitless) [Lower; Upper Confidence Interval]

2002 603 NIA 739,877 [506,889; 1,043,891]

2003 139 NIA 634,000 [340,811 ; 1,081,388]

2004 210 99.7 654,492 [370,200; 1,074,662]

2005 74 52.9 477,775 [308,015; 708,388]

2006 26 18.2 186,797 [133,663; 254,133]

2007 41 32.5 291,964 [155,148; 502,239]

2008 28 24.1 325,333 [147,533; 626,188]

2009 23 43.8 365,946 [151 ,439; 748,841]

2010 17 27.4 169,417 [106,837; 255,665]

2011 29 18.8 290,792 [99,502; 670,574]

2012 343 130.2 772,311 [ 420,904; 1,303,955]

2013 42 20.4 212,504 [95,804; 410,659]

2014 18 30.1 207,595 [110,373; 356,969]

2015 9 13.8 139,310 [66,314; 259,301]

2016 7 1.8 16, 159 [7,403; 30,886]

2017 8 3.8 47,786 [21,709; 91,864]

In addition to these abundance estimates, the CDFW conducts four fish surveys from which it develops indices of delta smelt' s relative abundance (Figures 1 and 2). Each survey has variable and unquantified capture efficiency, and in each, the frequency of zero catches of delta smelt is very high, largely due to the species' rarity (e.g., Latour 2016; Polansky et al. in press). The [summer] Townet Survey (TNS) is the longest running indicator of delta smelt relative abundance; it has been conducted since 1959. Although this survey was designed to index the relative abundance of metamorphosing juvenile striped bass (Morone saxatilis) (Turner and Chadwick 1972), delta smelt have been collected incidentally; most of the delta smelt captured are age-0 and about 20-40 mm in length (Miller 2000). The FMWT is the second longest running

Mr. Mark T. Ziminske 14 indicator of delta smelt relative abundance; it has been conducted since 1967. This survey was also designed to index the relative abundance of age-0 striped bass (Stevens 1977), but as with the TNS, delta smelt are collected incidentally (Stevens and Miller 1983). Most of the delta smelt captured by the FMWT are age-0 "subadults" and are about 50-70 mm in length (Sweetnam 1999). The 20-mm Survey is the third longest running indicator of delta smelt relative abundance; it has been conducted since 1995. This survey was designed to monitor the distribution of late larval or metamorphosing juvenile delta smelt to assess their distribution and risk of entrainment into the large water export diversions of the Central Valley Project (CVP) and State Water Project (SWP) (Dege and Brown 2004). As its name suggests, most of the delta smelt collected by the 20-mm Survey are about 10-30 mm in length, with a peak catch of fish just under 20 mm (Kimmerer 2008). The newest indicator of delta smelt relative abundance is the SKT Survey, which has been conducted since 2002. This survey was designed to monitor the distribution of pre-spawn and spawning adult delta smelt to assess their distribution and risk of entrainment. Most of the delta smelt captured in the SKT are 60-80 mm in length (Bennett 2005).

The TNS and FMWT abundance indices for delta smelt have documented the species' long-term decline, while the newer 20-mm and SKT abundance indices have generally confirmed the recent portions of the trends implied by the older surveys (Figures 1 and 2). During the period of record, juvenile delta smelt relative abundance has declined from peak levels observed during the latter 1970s (Figure 1 ), while subadult relative abundance was at its highest in 1970, and similarly high i.n 1980 (Figure 2). Juvenile and subadult abundance indices both declined rapidly dming the early 1980s, increased somewhat during the 1990s, and then collapsed in the early 2000s. Since 2005, the TNS and the FMWT have produced indices that reflect less year to year variation than their 20-mm and SKT analogs, but overall, the trends in both sets of indices are similar. Dming the past decade, each index has frequently reached new record low levels. The TNS index was 0.0 in 2015 and 2016, and the 2015 FMWT index and subsequent 2016 SKT index were record lows (about one half of one percent of the relative abundance recorded in 1970-1971).

I

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20 60 I 40

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- 20

0 0 1955 1965 1975 1985 1995 2005 2015

Year

Figure 1. Time series of the CDFW's summer TNS (black line; primary y-axis) and 20-mm Survey (gray line; secondary y-axis) abundance indices for delta smelt.

x 1400 C1J

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~ 1000

IL..

C1J - 800 m

~ 600

3! 400

1965 1975 1985 1995 2005

Year x Q)

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400 ~ t m

300 :0 tu>

200 ·=

V>

Figure 2. Time series of the CDFW's FMWT (black line; primary y-axis) and SKT (gray line;

secondary y-axis) abundance indices for delta smelt.

The abundance of adult delta smelt may have exceeded twenty million in 1980-1981 (Rose et al.

2013b ). This may sound like a large number - and it is compared to the contemporary estimates listed in Table 3. However, decades of monitoring by CDFW has shown that the delta smelt has usually not been very abundant when compared to other pelagic (meaning offshore-oriented or open-water) fishes (Figure 3). In the TNS, delta smelt catches have usually been lower than age- 0 striped bass, and in recent years, also lower than gobies and threadfin shad. In the FMWT, delta smelt catches have been persistently lower than at least five other species. Research and monito1ing in shallower habitats like Suisun Marsh (Moyle et al. 1986; Matern et al. 2002), Delta beaches (Nobriga et al. 2005), and small tidal marshes in the upper estuary (Gewant and Bollens 2012) have reported even lower relative abundances of delta smelt. In each of the studies cited, the catches of delta smelt represented less than one percent of the total fi sh catch and there were usually more than a dozen more abundant fi sh species.

100%

.c 80%

60% "'

40% GI -

bO

"' 20% ... c

GI .... .. 0% GI

Cl.

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• Northem Anchovy

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0 0 , O'l O'l .--1 .--I en en .--1

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American Shad

• Longtin Smelt Thre adfin Shed

Yellowfin Gobv

0 0 0 .--1 0 0 N N

Summer Tow-net Survey

100% -

80%

60%

40%

20%

0% l..O O'l .--I a Americiln Shad

Lcngf"1t1 Sm•lt

• hcri'ic Herring:

lhrtadfin Shad

• Dela Smelt

• N crthtrn Anchovy a Striped Soss ei:e-D

Fall MidwaterTrawl

Figure 3. Fractional compositions of the eight most frequently collected fish species in the CDFW's summer TNS (1959-2015), and the seven most frequently collected fish species in the FMWT (1967- 2015).

The long-term rarity of the delta smelt has had a consequence for understanding the reasons for their population decline, which generates uncertainty about how resource managers should intervene. Some pelagic fishes have shown long-term relationships between Delta inflow, Delta outflow and their abundance or survival (Stevens and Miller 1983; Jassby et al. 1995; Kimmerer 2002b; Kimmerer et al. 2009). There does seem to be some difference in the likelihood of whether the delta smelt population will increase or decrease in abundance from one year to the next based on hydrology (Figure 4), but there has never been any predictable relationship linking freshwater flow conditions to the relative abundance of delta smelt (Stevens and Miller 1983;

Jassby et al. 1995; Kimmerer 2002b; Kimmerer et al. 2009). Recently, several teams of researchers have built several varieties of conceptual (IEP 2015) and mathematical (Thomson et

al. 2010; Maunder and Deriso 2011 ; Miller et al. 2012; Rose et al. 2013a) life cycle models for the delta smelt that attempt to describe the reasons the population has declined. Some of these models have been able to recreate the trend observed in abundance indices very well (Figure 5), but they have all done so using different approaches and different variables to do so.

Collectively, these modeling efforts have been helpful in that they generally support water temperature and changes in the estuary's food web as 'universally supported ' factors affecting delta smelt. However, they have also come to very different conclusions about the conservation value of more readily manageable factors like water project operations.

I I

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Wet or Above-normal

Maybe down

Dry or Critical

Figure 4. Frequencies of delta smelt population increases or decreases (red colored portions of each bar occurring below zero) based on the CDFW's FMWT Survey, 1967-2015. A population increase reflects an increase in relative abundance over the prior year's index and a population decrease reflects a decrease in relative abundance compared to the prior year's index. The Service performed bootstrap resampling on each year's catch per tow to generate a mean catch per tow with 95 percent confidence intervals. This resulted in four possible outcomes: (1) a statistically significant increase in relative abundance from one year to the next in which the confidence intervals of the two years did not overlap ("Up"; solid blue bar segments), (2) a statistically non significant increase in relative abundance from one year to the next in which the confidence intervals of the two years overlapped ("Maybe Up"; lighter blue bar segments), (3) a statistically significant decrease in relative abundance from one year to the next in which the confidence intervals of the two years did not overlap ("Down"; solid red bar segments), or (4) a statistically non-significant decrease in relative abundance from one year to the next in which the confidence intervals of the two years overlapped ("Maybe Down"; lighter red bar segments). The counts in each of the four categories were combined by Sacramento Valley WY types except that below normal years were not plotted. The frequencies of population decline were converted into a negative number so that population increases would count up from the zero line on the y-axis and population decreases would count down from the zero line.

Maunder and Deriso (2011)

:: r~ j: 1' A f\_/\ J\

' I u ~ L;-VJV · ~\.. . 1970 ~• IO S'll) J'JllO J~') t W I~~ tCl.lO JC(tl tOIO

Thomson et al. (2010)

1900 1990

Year

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0 . . ' - ,.

i*.- ~ 1'11 1* 1#- ai&Xi Mt :i-~ 2t<I) no:. ~

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Rose et al. (2013a)

Figure S. Examples of recent published model fits to time series of delta smelt relative abundance data. The source of each is referenced above or alongside each time series. In each plot, observed catches are depicted as black dots and model predictions of the data as gray or black lines. Model predictions from Rose et al. (2013a) are a black line with open symbols. In Maunder and Deriso (2011), the three panels represent the 20-mm Survey, summer TNS, and FMWT Survey from top to bottom, respectively. The other three studies are fit to estimates of adult delta smelt relative abundance (FMWT catch in Thomson et al. 2010 and the FMWT index in Miller et al. 2012) or absolute abundance (Rose et al. 2013a). See each study for further details on Methods, Results, and the authors' interpretations of their results.

Habitat and Distribution

Because the delta smelt only lives in part of one comprehensively monitored estuary, its general distribution is well understood (Moyle et al. 1992; Bennett 2005; Hobbs et al. 2006, 2007;

Feyrer et al. 2007; Nob1iga et al. 2008; Kimmerer et al. 2009; Merz et al. 2011; Murphy and Hamilton 2013; Sommer and Mejia 2013). There are both location-based (e.g., Sacramento River around Decker Island) and conditions-based (low-salinity zone) habitats that delta smelt permanently occupy. There are habitats that delta smelt occupy seasonally (e.g., for spawning), and there are habitats that delta smelt occupy transiently, which we define here as occasional seasonal use. These include distribution extremes from which delta smelt are not collected every year or even in most years.

Mr. Mark T. Ziminske 19

Most delta smelt complete their entire life cycle within or immediately upstream of the estuary's low-salinity zone. The low-sahnity zone is frequently defined as waters with a salinity range of about 0.5 to 6 parts per thousand (ppt) (Kimmerer 2004). The 0.5 to 6 ppt and similar salinity ranges reported by different authors were chosen based on analyses of historical peaks in phytoplankton and zooplankton abundance, but recent physiological and molecular biological research bas indicated that the salinities that typify the low-salinity zone are also optimal for delta smelt (Komoroske et al. 2016). The low-salinity zone is a dynamic habitat with size and location that respond rapidly to changes in tidal and river flows. By local convention the location of the low-salinity zone is described as "X2" in terms of the distance from the 2 ppt isohaline to the Golden Gate Bridge. The U.S.