ENV Attachment 1 for reference.pdf

United States Department of the Interior

FISH AND WILDLIFE SERVICE

San Francisco Bay-Delta Fish and Wildlife Office

In reply refer to:

0SFBDT00-2017-F-0099

Mark T. Ziminske

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

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

JUL 31 2017

Subject: Formal Consultation on the Sacramento River Deep Water Shipping Channel Dredging and Bank Stabilization Project,. Sacramento, Solano, and Yolo Counties, California

Dear Mr. Ziminske:

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 Sacrainento River Deep Water Shipping Channel (SRDWSC) Dredging and Bank Stabilization Project (project), in Sacramento, Solano, and Yolo Counties. The proposed project is within and along the Deep Water Shipping Channel in the Sacramento 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 transpacijicus) 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 programmatic biological 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 ainended (16 U.S.C. 1531 et seq.) (Act).

This response is based upon information from: (1) the undated Sacramento 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 desc1iption; (4) the Service's August 12, 2016 BO on the 2016 Sacrainento and Stockton Deep Water Shipping Channels Dredging and Bank Stabilization Project (Service File No. 0SFBDT00- 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 I 00-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 SRDWSC project on the GOS, the delta smelt, and the delta smelt's critical habitat.

CONSULTATION HISTORY

August 12, 2016 The Service issued its BO for the 2016 SRDWSC project and Stockton Deep Water Shipping Channel (SDWSC) Operations and Maintenance Dredge Project.

November 2016- F ebruary 20 I 7

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

Sacramento River Deep Water Shipping Channel

The SRDWSC begins in the city of West Sacramento and extends southwest to the community of Collinsville in Solano County. The lower portion of the channel follows the natural channel of the Sacramento River and Cache Slough; the upper portion is manmade, extending overland to terminate at the Port of West Sacramento. The Port of West Sacramento facilities include a harbor and turning basin. The SRDWSC varies in width from 200 to 400 ft. The turning basin at the Port of Sacramento is triangularly shaped, being 3,100 ft long and 1,800 ft wide at the widest point. The ship channel was proposed to be deepened and widened as authorized under the Water Resources Development Act of 1986 (Public Law 99-662). The channel was proposed to be deepened from 30 ft to 35 ft below mean lower low water (MLLW) along its entire length and widened to bottom widths ranging from 250 to 400 ft. Due to funding and other constraints, the originally proposed project has not been completed. As of the beginning of 2014, only the upstream most 8 miles, river mile (RM) 35 to the turning basin, of the ship channel had been deepened and the only widening that occurred was that necessary to maintain a I :3 side slope for the deeper channel.

The SRDWSC includes the Sacramento-San Joaquin River confluence and estuary at the lower portion of the SRDWSC and habitat types are primarily riparian and riverine (fresh water). The

SRDWSC utilizes five different DMPSs: S-31, Grand Island, Rio Vista, Decker Island, and Augusto Pit. All the DMPSs are located adjacent to the shipping channel.

SRDWSC DMPSs

There are currently five DMPSs for the SRDWSC as shown in Table 1 and discussed in detail below. Table 2 shows the total site acreage dredged in the channel around each DMPS with the exception of Grand Island which has not been dredged since 2000 and does not have data.

Table 1. Sacramento Deen Water Shin Channel DMPSs Placement Method of Return Water

Point of Contact Special Landing Point; Line Site and Site Specifications Requirements Pump Allowance

Augusto Pit Gravity. Water leaves site P011 of West Site underlain by Station 274+00 (S-20) Class I by agricultural ditch with Sacramento/DWR peat Allowance ~2,100 ft Site pump out provided by

Reclamation District-341.

Ponding time: 52 hours (hrs) Ponding area: 30 acres (ac) Ponding vol: 96,800 cubic yards (cy)

Decker Island Gravity. Water leaves site Port of West Placement Station 368+00 (S-19) Class II by existing weir box. Sacramento around ongoing Allowance ~ 2,200 Site Ponding time: 825 hrs mmmg ft+ 1,300 ft

Ponding area: 320 ac operations. Only Ponding vol: 1,548,000 cy access to island Station 432+00 is by boat Allowance~ 2,200 ft + 1,000 ft

Rio Vista Gravity. Water leaves site Corps May have sand Station 518+00 (S-16) by existing weir box. trucks hauling Allowance ~ 900 ft + Class I Site Ponding time: 415 hrs through site; 2,100 ft

Ponding area: 140 ac Elevated site.

Ponding vol: 900,000 cy Station 586+00;

Allowance ~ 800 ft+ 1,200 ft

Grand Island Gravity. Water leaves site Corps Portion of Site is Station 795+00 (S-14) Class I by existing weir box. heavily wooded; Allowance ~ 1,300 ft Site Ponding time: 127 hrs elevated site

Ponding area: 73 ac Station 768+00 Ponding vol: 235,547 cy Allowance~ 450 ft

S-31 Class! Pump Port of West Long Narrow Station~ variable Site Ponding time: 415 hrs Sacramento Site; Landing Allowance~ 450 ft

Ponding area: 1020 ac point will move Ponding vol: 770,000 cy along site.

Mr. Mark T. Ziminske 4

Tb a le 2. ota acre eet re l!!e or eac T I f d d df bDMPS b etween 2000 d2013 an Sacramento DWSC (Acre Feet Dredged)

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

Decker 20 31 5 19 99 0 42 217 Island Rio 14 50 9 10 5 6 93 Vista S-31 261 85 87 150 24 27 40 69 22 72 836

Augusto 78 17 33 129 Pit Avg 98 65 11 53 0 92 74 12 26 40 39 13 0 39

Total 295 194 23 106 0 183 149 24 78 40 79 26 0 78

Augusto Pit, S-20

This DMPS is an approximately 60-acre site on Sherman Island that contains some shrub vegetation. The site contains a seasonal wetland along with an adjacent toe drain. The site has been used as a DMPS in 2001, 2002, and 2005.

Decker Island, S-19

This DMPS is an approximately 590-acre site located on the Jersey Island United States Geological Survey (USGS) quadrangle map in Solano County. The site is located in the central west portion of Decker Island in the vicinity of a commercial sand mining operation. The great majority of the area consists of sand spoils from previous dredging operations and is partially vegetated with common herbaceous species. The back portion (eastern side) of the island contains a seasonal wetland and holding pond, both of which are potential GGS habitat. Dredged materials would be placed on the non-wetland areas of this site. This site was used as a DMPS in 2000, 2006, 2008, 2010, 2011, and 2013.

Rio Vista, S-16

This DMPS is an approximately 80-acre site located on the Rio Vista USGS quadrangle map in Solano County. The site is a seasonal wetland according to the National Wetlands Inventory map. Dredged material would be placed in non-wetland areas of this site. The water that carries the material would drain into the wetland areas and eventually recede via a culvert into the river.

This site has been used as a DMPS in 2000, 2006, 2008, 2010, 2011, 2013, and 2015.

Grand Island, S-14

This DMPS is an approximately 220-acre site located on the southern tip of Grand Island at the confluence of the Sacramento River, Steamboat Slough, and the SRDWSC. There are shallow ponds adjacent to the Sacramento River and Steamboat Slough. Water is available year-round from the rivers, runoff and seepage. There is agricultural land adjacent to the site. The site has not been used since 2000.

S-31

This DMPS is an approximately 1,020-acre site located along the western bank of the SRDWSC between the channel and the Yolo Bypass. The site extends from where the channel meets the Yolo Bypass levee for 19 .5 levee miles to where the channel rejoins the Sacramento River. The lower slope of the ship channel is vegetated by a mosaic of emergent vegetation at the water's edge with grasses, scattered willows, and blackberry bushes higher up the levee slope. The berm area is the portion of the site that would be used for the placement of dredged material. The majority of the benn area is vegetated with grasses and is grazed by cattle and goats.

Purpose and Need for Maintenance Dredging and Bank Stabilization

The Corps proposes to continue to perform routine maintenance dredging and bank protection on the SRDWSC under Indefinite Delivery/Indefinite Quantity (IDIQ) 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 SRDWSC 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 West Sacramento 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 in the Yolo Bypass.

The Corps proposes to conduct its annual operations and maintenance dredging in the SRDWSC during the 5-year term beginning approximately August 1 and finishing approximately October

31. Prior to each dredging season, the Corps will coordinate with the Service. This would include documentation of exact reaches of the SRDWSC 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 SRDWSC 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 MLLW

• The upper p01iion of the channel would be maintained at a depth of35 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.

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 (CVR WQCB) 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 cutterhead 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 SRDWSC. 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 SRDWSC, 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 SRDWSC 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. The Corps proposes to conduct bank stabilization between June 15 and November 30.

Proiect 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 SRDWSC.

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.

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 I 0-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.

I 0. Since maintenance dredging and bank protection work near potential GGS habitat(s) may occur up to November 30, beyond the GGS October I work-window limit, the Corps will notify the Service of potential work that may affect GGS. A Service approved biological monitor will survey the bem1ed 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

Mr. Mark T. Ziminske 9 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 CVR WQCB constituents of concern and physical parameters. Management practices will include placing flash boards at the spillway ofDMPS 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 (WDR) 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 SRDWSC, with their associated river banks in the Sacramento River, as well the five DMPSs within the legal California Delta (See Attachments for maps). This constitutes approximately 592 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 five DMPSs (See table 2). Grand Island has no data from 2000; however, it is similar in size and volume to Augusto Pit. The Service used the maximum volume dredged for Augusto Pit (78 acres) compared to the acres of this DMPS (60 acres) in a ratio to calculate the approximate total estimated maximum volume dredged for Grand Island DMPS. Augusto Pit is approximately 60 acres and dredged 78 acres. In relation, Grand Island is 80 acres and using the same ratio it is estimated that Grand Island would have a maximum dredging volume of I 04 acres. There are approximately 2,088 terrestrial acres for the five DMPSs. This is based on the total ponding area of the five DMPSs.

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 threatened to endangered (Service 201 0a). A 12-month finding on a petition to reclassify the delta smelt as an endangered species was completed on April 7, 2010 (Service 201 Ob). 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 2010c). 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/doc3 570.pdf and http://www.gpo.gov/fdsys/pkg/FR- 2013-1 l-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) 201 7 appears to be at its second lowest abundance on record, the lowest having been recorded dming WY 2016 (Table 2). The 2016 Fall Midwater Trawl (FMWT) Index was 7, the second lowest on record. The CDFW Spring Kodiak Trawl (SKI) 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 SKI Abundance Index is 3.8, the second lowest on record. The Service calculated an absolute abundance estimate1 for

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

Mr. Mark T. Ziminske 11 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 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 suggest the population will continue to be ,mlnerable to stochastic events and operational changes that may occur in response until successive years of increased population growth results 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 the Service calculates from the s KT survev.

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 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 12

[summer] Townet Survey (TNS) is the longest rnnning indicator of delta smelt relative abundance; it has been conducted since 1959. Althougb this survey was designed to index the relative abundance of metan1orphosing juvenile striped bass (Marone 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 rnnning 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 rnnning 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-tenn decline, while the newer 20-mm and SKT abundance indices have generally confirn1ed the recent portions of the trends implied by the older surveys (Figures I 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 in 1980 (Figure 2). Juvenile and subadult abundance indices both declined rapidly during 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. During 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 ).

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1955 1965 1975 1985

Year 1995 2005

I 20

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.

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3: 1200

~ 1000 ...

Cl) : .... 800 .

"' 3:

"C 600 ~ 8?. 400

0 ........... -

1975 1985 1995 2005 Year

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-

Mr. Mark T. Ziminske 14

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 monitoring 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 fish catch and there were usually more than a dozen more abundant fish species.

100%

.c 80% u ..

60% .. ., 40% ., 20% ..

C ., ~ 0% ., ... en

LI)

en .-1

~ Age-0 Striped Bass

■ DeJta Smelt

■ Northern Anchovy

Tridentlger spp_

0 0

" C() en en .-1 .-1

0) 0) .-1

Year

13\ American Shad m tongfin Smelt \\ Threadfin Shad w Yellowf;n Goby

0 0

8 .-1

N N

Summer Tow-net Survey

100%

80%

60%

40% , 20%

0%

" l.O en .-1

Wi Amerlcen Shad longfin Sme!t m: Pacific Herring

1, Threadfin Shad

C()

" en .-1 m 00 m .-I

■ Delta Smelt a Northern Anchovy

II Striped Sass age-0 en en en .-1

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 I 983; 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. 201 0; 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.

fl iii

"tl

§ -5 iil "tl ., "' m -10 t; ., ' v -15

Ill Up Maybe Up

Wet or Above-normal

Down 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 iu 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)

Thomson et al. (2010)

- 0.50 a.

0.25 0.

L---"-i ___ ......_,,..w..1.,..-........._,......~--......... UJ..1...........J

1970 HJBO 1900

:; '"' Miller et al. (2012)

·A •

Year

0, , " T 799\ 1'1% 1%1 1s".\\\ \%'!> :,'(,•~~ 20Q! i'OU /:'XiS :h.10J ;KXO:, Yea•

Rose et al. (2013a}

Figure 5. Examples ofrecent published model fits to time series of delta smelt relative abundance data. The source of each is referenced above or alongside each time series. Iu each plot, observed catches are depicted as black dots aud 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; Nobriga 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 17

Most delta smelt complete their entire life cycle within or immediately upstream of the estuary's low-salinity zone. The low-salinity 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 has 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. Environmental Protection Agency (EPA) recently finished a comprehensive set of maps that show how the low-salinity zone changes in size and shape when freshwater flows change the location ofX22

. The low-salinity zone expands and moves downstream when river flows into the estuary are high, placing low-salinity water over a larger and more diverse set of nominal habitat types than occurs under low flow conditions. During periods oflow outflow, the low-salinity zone contracts and moves upstream. Due to its historical importance as a fish nursery habitat, there is a long research history into the physics and biology of the San Francisco Estuary's low-salinity zone (Kimmerer 2004).

The ecological function of the low-salinity zone also varies depending mainly on freshwater flow (Jassby et al. 1995; Kimmerer 2002a; Kimmerer 2004). Low outflow can decrease the capacity of the low-salinity zone and adjacent habitats to support the production of delta smelt by reducing habitat diversity and concentrating the fish with their predators and competitors (Service 1993, 1994). During the past four decades, the low-salinity zone ecosystem has undergone substantial changes in turbidity (Schoellhamer 2011) and food web function (Winder and Jassby 2011) that cannot be undone solely by increasing Delta outflow. These habitat changes, which extend into parts of the Delta where water is fresher than 0.5 ppt, have also decreased the ability of the low-salinity zone and adjacent habitats to support the production of delta smelt (Thomson et al. 2010; Rose et al. 2013b; IEP 2015).

Delta smelt have been observed as far west as San Francisco Bay, as far north as Knights Landing on the Sacramento River, as far east as Woodbridge on the Mokelumne River and Stockton on the Calaveras River, and as far south as Mossdale on the San Joaquin River. This distribution represents a range of salinity from essentially zero ppt up to about 20 ppt, which represents a salinity range well beyond definitions of the low-salinity zone or mixing zone near a salinity of2 ppt emphasized in the critical habitat rule (Service 1994). It is also well beyond the geographic extent of the critical habitat rule (described below). However, most delta smelt that have been collected in the extensively surveyed San Francisco Estuary have been collected from locations within the bounds defined in the critical habitat rule. In addition, all habitats known to be occupied year-around by delta smelt occur within the bounds defined in the critical habitat rule.

Delta smelt permanently occupy the Cache Slough 'Complex', including Liberty Island and the adjacent reach of the Sacramento Deepwater Shipping Channel (Sommer and Mejia 2013), Cache Slough to its confluence with the Sacramento River and the Sacramento River from that confluence downstream to Chipps Island, Honker Bay, and the eastern part of Montezuma Slough (Figure 6). The reasons delta smelt are believed to pe1manently occupy this part of the

2http://www.waterboards.ca.gov/waterrightslwater _issues.1programs/bay _Delta/docs/ cmnt081 712/karen _ schwinn.pd f

Mr. Mark T. Ziminske 18 estnary are the year-round presence of fresh- to low-salinity water that is comparatively turbid and of a tolerable water temperature. These appropriate water quality conditions overlap an underwater landscape featuring variation in depth, tidal current velocities, edge habitats, and food production (Sweetnam 1999; Nobriga et al. 2008; Feyrer et al. 2011; Murphy and Hamilton 2013; Hammock et al. 2015; Bever et al. 2016). Field observations are increasingly supported by laboratory research that explains how delta smelt respond physiologically to variation in salinity, turbidity, water temperature, and other aspects of their habitat that can vary with changes in climate, freshwater flow and estuarine bathymetry (Hasenbein et al. 2014; 2016; Komoroske et

al. 2014; 2016).

Each year, the distribution of delta smelt seasonally expands when adults disperse in response to winter flow increases that also coincide with seasonal increases in turbidity and decreases in water temperature (Figure 6). The annual range expansion of adult delta smelt extends up the Sacramento River to about Garcia Bend in the Pocket neighborhood of Sacramento, up the San Joaquin River from Antioch to areas near Stockton, up the lower Mokelumne River system, and west throughout Suisun Bay and Suisun Marsh. Some delta smelt seasonally and transiently occupy Old and Middle river in the south Delta each year, but face a high risk of entrainment when they do (Grimaldo et al. 2009).

Adults in kodiak trawls sampling offshore surface waters, January-May larvae in 20-mm trawls sampling offshore water columns, April-June

Adults in beach seines sampling very close to shorelines, March-April

Juveniles ln midwater trawls sampling offshore water columns, September December

Figure 6. Maps of multi-year average distributious of delta smelt collected in four monitoring programs. The sampling regions covered by each survey are outlined. The areas with dark shading surround sampling stations in which 90 percent of the delta smelt collections occurred, the areas with light shading surround sampling stations in which the next 9 percent of delta smelt collections occurred. Source: Mnrphy and Hamilton (2013).

Mr. Mark T. Ziminske 19

The distribution of delta smelt occasionally expands beyond this area (Figure 6). For instance, during high outflow winters, adult delta smelt also disperse west into San Pablo Bay and up into the Napa River (Hobbs et al. 2007). Similarly, delta smelt have occasionally been reported from the Sacramento River north of Garcia Bend up to Knights Landing ( e.g., Merz et al. 2011;

Vincik and Julienne 2012).

The expanded adult distribution initially affects the distribution of the next generation because delta smelt eggs are adhesive and not believed to be highly mobile once they are spawned. The distribution of larvae reflects a combination of where spawning occurred and freshwater flow conditions when the eggs hatched. Variation in Delta outflow affects the spatial distribution of the delta smelt population for most of its life. The ecological condition of the estuary's low salinity zone has historically been indexed using a statistic called X2, a local name for the geographic location of2 ppt salinity near the bottom of the water column (Jassby et al. 1995).

During spring, larval…