Biological Opinion.pdf

United States Department of the Interior

FISH AND WILDLIFE SERVICE

San Francisco Bay-Delta Fish & Wildlife Office

650 Capitol Mall, Suite 8-300

Sacramento, California 95814-4700

In reply refer to:

2023-0018865-S7-001

June 28, 2023

Mr. Marshall K. Harper

Chief, Environmental Resources Branch

United States Department of the Army

Army Corps of Engineers, Sacramento District

1325 J Street

Sacramento, California 95814-2922

Subject: Reinitiation of Consultation for the Sacramento River Deep Water Shipping

Channel Dredging and Bank Stabilization Project, Sacramento, Solano, and Yolo

Counties, California (Service File No. 08FBDT00-2017-F-0099)

Dear Mr. Harper:

This letter is in response to the U.S. Army Corps of Engineers’ (Corps) January 30, 2023, letter requesting reinitiation of formal consultation with the U.S. Fish and Wildlife Service’s (Service) on the Sacramento River Deep Water Shipping Channel Dredging and Bank Stabilization Project

(project), Sacramento, Solano, and Yolo Counties, California (Service File No. 08FBDT00-

2017-F-0099) (July 31, 2017 BO). Your request was received via electronic mail (email) on

January 30, 2023. The Corps is proposing to extend the consultation for 5 years covering dredge seasons 2023-2028 to incorporate mechanical clamshell dredging in addition to maintenance dredging conducted with a cutterhead hydraulic suction dredge on the Sacramento River Deep

Water Shipping Channel (SRDWSC). The Corps has determined the proposed project will likely adversely affect the federally threatened giant garter snake (Thamnophis gigas) (GGS), the federally threatened delta smelt (Hypomesus transpacificus) and its designated critical habitat. In addition, the Corps is requesting a conference opinion on the San Francisco Bay-Delta distinct population segment (DPS) of the longfin smelt (Spirinchus thaleichthys), which is proposed for listing as endangered under the Endangered Species Act of 1973, as amended (16 U.S.C. 1531 et seq.) (Act). This response is provided under the authority of the Act, and in accordance with the implementing regulations pertaining to interagency cooperation (50 CFR 402).

In reviewing this project, the Service has relied upon: (1) the Corps’ January 30, 2023, letter requesting reinitiation of the July 31, 2017 BO; (2) the January 2023 Programmatic Biological

Assessment for the Sacramento Deep Water Ship Channel Maintenance Dredging and Bank

Mr. Marshall K. Harper 2

Protection Project, Sacramento, Solano, and Yolo Counties, California (BA) prepared by the

Corps; (3) the September 2022, Sacramento River Deep Water Ship Channel Maintenance

Dredging and Bank Protection Project Biological Assessment Addendum for Beneficial

Reuse/Mechanical Dredging Pilot Project prepared by Anchor QEA; (4) the July 31, 2017, biological opinion (Service File No. 08FBDT00-2017-F-0099); (5) the March 14, 2022 one-year extension of the consultation for the project; (6) several emails, telephone conversations between the Service, the Corps, and their consultant; and (7) other information available to the Service.

The remainder of this document represents the Service's biological opinion on the effects of the

2023-2028 5-year implementation of the SRDWSC project on the GGS, the delta smelt, and the delta smelt's critical habitat and the Service’s conference opinion on the longfin smelt.

Consultation History

July 31, 2017 The Service issued the BO for the project.

March 13, 2019 The Service received the Corps’ March 8, 2019 request for reinitiation to extend the in-water work window.

October 30, 2019 The Corps, Service, and National Marine Fisheries Service (NMFS) met to discuss the extensions to the listed species in-water work windows.

October 31, 2019 The Corps withdrew the March 8, 2019 reinitiation request.

January 19, 2022 The Corps requested a one-year extension for the project’s consultation to dredge in 2022 with the intent to reinitiate for the next 5-year dredging program in the fourth quarter of fiscal year

2022.

March 14, 2022 The Service issued a one-year extension for the project’s consultation to dredge in the calendar year 2022 work window of

August 1 through October 31.

July 21, 2022 The Corps sent the Service an email informing the Service that they were evaluating a Value Engineering Study on the SRDWSC for the

2022 dredging season where they would propose to use clamshell dredging for parts of the channel and the dredged material would be reused beneficially at the Montezuma Wetlands.

August 11, 2022 The Service met with representatives from the Corps, NMFS, and the consultants to discuss the pilot project and provide technical assistance.

Mr. Marshall K. Harper 3

September 15, 2022 The Service received a request from the Corps to reinitiate formal consultation on the July 31, 2017 BO for the 2022 calendar year extension.

October 22, 2022 The Service issued the amendment to the July 31, 2017 BO.

January 30, 2023 The Service received the request to reinitiate the July 17, 2017 BO for dredging in years 2023 through 2028.

February 2, 2023 The Corps and the Service held a telephone conversation about species effects determinations and an effects determination for the delta smelt’s critical habitat for the project. The Corps was changing their determinations for the San Joaquin kit fox (Vulpes macrotis mutica), the valley elderberry longhorn beetle

(Desmocerus californicus dimorphus), and the California least tern

(Sterna antillarum browni), and that they were changing their determination for the delta smelt’s designated critical habitat from may affect, but not likely to adversely affect to may affect and is likely to adversely affect, but would not adversely modify the critical habitat.

June 6, 2023 The Corps sent the Service an email confirming the February 3, 2023, telephone discussion that the Corps had changed the determinations to “no effect” for the San Joaquin kit fox, the valley elderberry longhorn beetle, and the California least tern. The Corps also confirmed from the February 3, 2023, discussion that they had changed their determination for the delta smelt’s designated critical habitat from may affect, but not likely to adversely affect to may affect and is likely to adversely affect, but would not adversely modify the critical habitat.

BIOLOGICAL AND CONFERENCE OPINION

Description of the Proposed Action

The Corps proposes to continue routine maintenance dredging and bank protection on the

SRDWSC. The proposed action includes dredge work using hydraulic or mechanical dredging methods. The exact methods could include hydraulic cutterhead pipeline, mechanical bucket, or mechanical backhoe dredging and would depend on the contractor and site conditions. The rock placement would be accomplished with a clamshell crane with rock transported via barges, or by truck, depending on site conditions. The dredged material would be deposited at previously authorized dredging material placement sites (DMPS) (Table 1) and one new proposed DMPS.

Dredge slurry would be routed to the DMPS via pipelines or barges. The DMPS would be diked to allow dredge slurry to settle and consolidate. Decant water would then be discharged back into the SRDWSC, as determined during annual coordination with the Corps, dredge contractor, and

Mr. Marshall K. Harper 4 the Central Valley Regional Water Quality Control Board (CVRWQCB). Dredged spoils would be allowed to dry in the DMPS. 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. The proposed action would follow specific work windows to minimize impacts to species.

Table 1. SRDWSC DMPS, listed in order going upstream, with the proposed site.

Placement

Site

Area

(acres)

Method of Return

Water

Point of

Contact

Special

Requirements

Landing Point;

Line Pump

Allowance

Montezuma

Wetlands

(proposed)

(Phase II)

Gravity. Water leaves site through return water channel, which conveys it to the make-up pond.

Montezuma

Wetlands, LCC

Habitat restoration site; Off-loading by barge/scow only

Station number

2+00;

Augusto Pit

(S-20)

60 Gravity. Water leaves site via agricultural ditch with pump out provided by RD-341.

Ponding time: 52 hours

Ponding vol: 96,800 cubic yards

Port of West

Sacramento/

California

Department of Water

Resources

(DWR)

Site underlain by peat

Station number

274+10;

Allowance 2,100 feet

Decker Island

(S-19)

320 Gravity. Water leaves site by existing weir box.

Ponding time: 825 hours

Ponding vol: 1,548,000 cubic yards

Port of West

Sacramento

Placement around ongoing mining operations. Only access to island is by boat; elevated site

Station number

368+00;

Allowance 2,200 feet + 1,300 feet

Station number

432+00;

Allowance 2,200 feet + 1,000 feet

Rio Vista

(S-16)

140 Gravity. Water leaves site by existing weir box.

Ponding time: 415 hours

Ponding vol: 900,000 cubic yards

U.S. Army

Corps of

Engineers

May have sand trucks hauling through site;

elevated site

Station number

518+00;

Allowance 900 feet + 2,100 feet

Station number

586+00;

Allowance 800 feet + 1,200 feet

Grand Island

(S-14)

228 Gravity. Water leaves site by existing weir box.

Ponding time: 127 hours

Ponding vol: 235,547 cubic yards

U.S. Army

Corps of

Engineers

Portion of the site is heavily wooded;

Elevated site

Station number

795+00;

Allowance 1,300 feet

Station number

768+00;

Allowance 1,100 feet

S-31 1020 Pump.

Ponding time: 415 hours

Ponding vol: 770,000 cubic yards

Port of West

Sacramento

Landing point will move along site;

Portions of site are heavily vegetated with limited inundation permitted per task order

Station number variable;

Allowance 450 feet

Mr. Marshall K. Harper 5

Dredging methods

Prior to each proposed dredging season, the Corps will coordinate with the Service, NMFS, and the California Department of Fish and Wildlife (CDFW). This coordination will include documentation of exact reaches of the SRDWSC to be dredged, schedule for that dredging year, and which DMPS would likely be used. If there are changes to DMPS boundaries, location, or function, separate documentation will be provided to the agencies for approval. A maintenance dredging work window is proposed to follow a yearly schedule from August 1 through October

31 for the SRDWSC. A standard 2-week extension is also proposed, after concurrence with the

Service and NMFS, extending dredging in the SRDWSC to November 15, on a case-by-case basis. All sites would be dredged to maintain the current depth: the lower portion of the channel would be maintained at a depth of 30 feet below mean lower low water (MLLW), and the upper portion of the channel would be maintained at a depth of 35 feet below MLLW. An allowable over depth of 1 or 2 feet 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 proposed project will use hydraulic or mechanical methods for dredging. Dredged material would be routed to the DMPS via pipelines or barges. The 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 is done only with prior approval from the CVRWQCB in accordance with the 401 Water Quality Certification. Dredged spoils would be allowed to dry, and the land returned to prior uses except for Montezuma, where the dredged spoils would be used to create wetland habitat.

The CVRWQCB sets the standards for water quality within the Action Area. Dredging operations have to meet the water quality criteria and monitoring requirements described in the

Memorandum of Understanding between the United States Army Corps of Engineers, San

Francisco District and the California Regional Water Quality Control Board, Central Valley

Region, Concerning Operations and Maintenance Dredging of Stockton and Sacramento Deep

Water Ship Channels (MOU). The MOU requires water quality monitoring up and down current of the dredge, at the DMPSs, and at and up and down current of any discharge location back to the river from a DMPS. Water quality must be maintained and meet the turbidity and other criteria laid out in the MOU.

The quantity of material to be dredged each dredging season is expected to not exceed 500,000 cubic yards (cy), barring monumental flood events. Dredging is expected to operate 24 hours a day, seven days a week during the work window.

Hydraulic Cutterhead Pipeline

Hydraulic dredges remove and transport sediments by suction and pumping, which mixes large volumes of water with the sediment to form a slurry that is piped or barged to a disposal area. A hydraulic cutterhead pipeline dredge is a barge-type vessel that consists of an onboard pump(s), spud piles (long pipes), and a toothed cutterhead attached to a pipeline. The cutterhead is

Mr. Marshall K. Harper 6 mounted to a ladder that can be lowered, raised, and angled to increase the dredge path. The discharge pipeline exits the back (stern) of the dredge. Flexible pipeline sections are added to the dredge’s pipeline opening, as needed, depending on the distance between the dredge site and the

DMPS. Approximately every 500 feet, the flexible pipeline sections are anchored in the bottom of the channel using spud piles. Pipeline sections and anchors not in use would either be secured on a floating barge, capped and lashed together to float in the channel, or stored at the designated staging areas. Once the dredge is positioned, the pipeline and cutterhead would be lowered to the bottom of the channel. The cutterhead would then slowly start to rotate and break up sediment along the seafloor, continuing from side to side in a sweeping arc using the swing anchor. The dredge would move along the channel self-propelled or by tugboat, and a crew would always maintain and operate the dredging equipment. Skiffs and a tugboat would be used for crew transport, maintenance, and other operations associated with dredging activities. The collected dredge slurry is expected to consist of 80 to 90 percent water and 10 to 20 percent solids by weight. This ratio is ultimately determined by the difficulty of material removal experienced by the dredge operator.

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.

Dredging activities would be limited to depths greater than 25 feet, and the cutterhead would be kept within three feet 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 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 water sampling upstream and downstream of the dredge.

Mechanical Clamshell

A mechanical clamshell dredge consists of a crane mounted on a floating deck barge, with a clamshell bucket on the end of the crane boom. The deck barge has two to four spud piles attached to the platform, generally at the corners. The spud piles are long pipes that would be driven vertically into the SRDWSC bottom by hydraulic assistance. The spud piles are used to anchor the dredge barge. Clamshell dredges are not self-propelled, so they require a tugboat to tow or push the dredge to and from the dredge sites. Once a tug moves the dredge into place, the spuds are driven into the bay bottom anchoring the dredge. Once the dredge is anchored in place, dredging can begin. Relocating the dredge would require approximately one hour to complete.

On average, the mechanical clamshell dredge plant for this project would need to be relocated approximately every three hours. In addition, when working in the ship channel, the dredge

Mr. Marshall K. Harper 7 would need to be moved out of the shipping channel to allow deep draft vessels to transit the channel.

The crane would be equipped with a boom that is long enough to extend out beyond the end of the work barge in any direction and is able to swivel 360 degrees on its mount. A large clamshell bucket would be attached to the end of a series of cables at the end of the boom, which would allow the bucket to be raised and lowered into the water. The cables would open and close the bucket as it is filled with sediment and then emptied into scows. Scows are open barges that can carry large quantities of sediment and are towed with tugboats to and from disposal sites. As soon as one scow is filled and hauled away, another empty scow would be maneuvered into place alongside the dredge and digging would continue.

Clamshell buckets would be raised and lowered to the bottom of the SRDWSC using a system of cables. The weight of the bucket would be sufficient for it to fall through the water column into the bottom sediment. Cables would restrict the clamshell from going too deep, or beyond the maximum allowable overdepth. During mechanical dredging, the clamshell would close and be pulled up through the water column to above the scow. Once over the scow, the clamshell would open and deposit the dredged material into the scow. The bucket’s full cycle would take approximately 75 seconds from entry into the water column, capturing sediment in the bucket, raising in the water column, and dropping sediment into the scow; for approximately 25 seconds of the cycle the bucket would be below water. When all the material within reach of the clamshell is dredged, the spuds would be raised, and the tender tug would transport the dredge and scow to the next area requiring dredging. The process would be repeated until all material is dredged from the channel. Following dredging, hydrographic surveys would be conducted to ensure that the entire area is dredged to the desired depth.

During dredging, clamshells would place a slurry of sediment and water in the scows. Depending on the sediment type being dredged, the sediment-to-water ratio of the slurry is expected to be approximately 60 to 70 percent sediment and 30 to 40 percent water. To increase the sediment volume in the scows, the scows may decant water back to the water column in a process called overflow. Overflowing the scows increases the sediment volume, compared to water, which can decrease the number of scow-tug trips to placement sites, thereby decreasing construction costs.

Turbidity monitoring would be conducted within 500 feet of dredging operations to demonstrate that the turbidity plume generated by overflow activities meet the turbidity and other criteria laid out in the MOU.

Based on prior dredging seasons, most of the dredge material within the SRDWSC is comprised of sand and silt, which settles within a couple of hours. Based on 12 samples, eight had sediment that was greater than 85 percent sand and silt (Corps 2021). Percent clay content increased closer to the Port of West Sacramento (around Station 1440) and reached a maximum of 44 percent clay within Station 1620 (Corps 2021).

For the proposed project, the clamshell bucket capacity would range between 20 to 50 cy, depending on dredge availability. Up to seven scows, with a capacity of 2,000 to 4,000 cy, and up to four 1,800-horsepower (hp) tugs would be used to transport dredged material to placement sites. In addition, one 1,000 hp tender tug would be required to maneuver each dredge plant.

Mr. Marshall K. Harper 8

The estimated daily production rate would range between 3,000 and 7,000 cy, depending on the location of dredging and the DMPS being used. For example, the production rate would be approximately 5,000 cy if a nearby DMPS was available, while the production rate would decrease if material would have to be transported further.

Dredge Material Transport and Placement

For hydraulic cutterhead dredging, the dredge material would be transported to the DMPS via discharge pipes. Mechanical dredging would use scows to transport the dredged material to the

DMPS.

Scows transported to the DMPS would moor to an offloader at the respective site, such that sediment could be pumped out of the scow and onto the restoration site. The dredged material would be pumped out using a modified hydraulic pipe dredge, which serves as an offloader. A

Liberty offloader, which is on a floating barge or a land-based offloader could be used. Once moored, the offloader would insert a snorkel into the scow, simultaneously injecting water into the scow to create a water-sediment slurry and pumping the slurry from the scow to a designated cell within the site. The offloader's water intake system must be screened in accordance with the

CDFW's screening criteria. It would take approximately two hours to completely offload dredged sediment from a scow. Scows-tugs would travel an average of 20 miles to the DMPS. Scows-tugs would travel approximately 7 knots (8 miles per hour) from dredge sites to the DMPS. On average, each scow-tug trip to and from the beneficial use sites, including offloading, would take approximately 1-3 hours.

The discharge pipeline would run from the dredge in the channel, across the bank, and onto the relevant DMPS. At all DMPS, a nominal area of outboard levee 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. All pipes would be placed so as to avoid affecting any listed species or habitat.

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. Depending on which section is being dredged, the length of the pipeline could range from 1,500 to 22,000 feet. The dredge contractor would determine the best route for the pipeline (per the disposal plan) in conjunction with a qualified biologist to avoid special status 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 Protection

Suitable rock protection would be placed at eroded sites. Where scour, wash, settlement, or failure of a portion of the original stone 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

Mr. Marshall K. Harper 9 be filled with earth that is free from brush, roots, sod, or other unsuitable material and additional stone would be placed upon the earth fill. Bank stabilization maintenance work would bring the rock protection to its original section, using rock fill, filter material, and quarry rock. To the extent practicable, the rock would be similar in kind and gradation.

Along reaches of the SRDWSC where filter material was originally placed or where it may be required, maintenance repair of existing 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 will alter the slope to conform with standards by placing rock, as needed, to protect completed works.

Construction activities in shallow water habitats will 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 constructed portion of the SRDWSC at various locations. Rock may be placed at any site that previously contained bank protection work or where there is a need for additional rock due to bank erosion.

The Corps will conduct bank protection maintenance during the work window from June 15 to

November 30 to avoid adverse effects to listed fish species in the project area, including Delta

Smelt.

Fish entrainment and/or capture monitoring

Depending on the type of dredging conducted, the dredge contractor will employ one of the below listed fish entrainment/capture monitoring programs.

A fish entrainment monitoring program has been implemented to help 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 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 dredged material monitoring and further reduce adverse effects. Entrainment monitoring will be implemented during each dredging season unless otherwise noted by the Service, NMFS, and CDFW. Overall monitoring time will be increased to reach a goal of at least 30 percent of dredged material monitored during any given dredge season.

The protocol for entrainment monitoring is well-developed for use with a hydraulic cutterhead dredge; however, entrainment monitoring is less successful when conducting maintenance dredging utilizing a clamshell dredger. Accordingly, the Corps proposes to conduct experimental fish capture monitoring to identify a method which could be used to quantify take of special status fish and other organisms. Refinements to these protocols would occur through the adaptive management process through close coordination with the Service throughout the dredge season.

Mr. Marshall K. Harper 10

Since the variation in the material composition is unknown, and the variation in the benthic biota and fish captured is also unknown, the Corps is proposing to use grid sampling to gain an understanding of the level of variation in the material. Since the capacity of a standard scow is

5000 cubic yards, and the standard environmental bucket can transport 30 cubic yards, each scow can carry approximately 167 bucket loads. Thirty percent of this value, the target under the other protocol, is 50. Therefore, taking 50 samples of a full scow is intended to simulate taking a grab sample of 30 percent of the loads delivered to the scow. At this juncture, this sampling protocol will help the Corps understand the variation present in the medium and the organisms captured, while meeting targets similar to those under the hydraulic monitoring protocol. After variation is understood, the Corps, in coordination with NMFS will revise the protocol to determine a statistically significant number of samples to take per scow.

Scow Grab Sampling

1. Once a scow is full, visually divide the scow into 1-yard x 1-yard square grids.

Number each grid sequentially.

2. Utilizing a random number generator, select and identify 50 individual grid squares from the scow.

3. Utilizing another random number generator, assign a random depth to the nearest half-foot ranging from surface (0) to full depth (usually 8.5 feet) to each of the individual grid squares identified in the previous step.

4. Utilizing a grab sampler no smaller than 1 cubic foot in size, collect a sample of sediment from the scow for each of the individual grid squares identified.

5. Characterize the spoil material (e.g., sand, silt, or clay). Separate any incidentally collected organisms from other attendant material. Record any fish or invertebrates incidentally collected including all pertinent attributes documented under the hydraulic fish entrainment monitoring program.

6. Document all findings in the Biological Resources Monitoring Report.

Engineering Research and Design Center Fish Screen

The Corps Engineering Research and Design Center is currently in the process of designing a fish monitoring screen for use with mechanical dredgers which would function similarly to the fish entrainment monitoring device in use for hydraulic dredgers. To further this effort to quantify take of listed species in real time, maintenance dredging completed under this project would utilize the experimental device and provide reports to determine the feasibility of permanently including this monitoring measure.

Mr. Marshall K. Harper 11

Avoidance and Minimization Measures

The Corps is proposing to implement a number of general conservation measures such as standard Best Management Practices (BMPs) and other measures. Please refer to the project BA for these BMPs. The following conservation measures are specific with regard to the delta smelt, the longfin smelt, and the GGS.

Delta Smelt and Longfin Smelt

All dredging will be accomplished during an in-water work window from August 1 to October

31. The recommended work window for the delta smelt is August 1 through November 30;

however, the Corps is observing the October 31 window end date for protection for species under

NMFS’ regulatory responsibility.

Dredging Operations-Related Avoidance and Minimization Measures:

1. No dredging work will be conducted from land-based equipment.

2. Dredging at depths of less than 20 feet will be avoided to the maximum extent achievable.

3. Maintenance dredging will only be conducted in the authorized channel to the authorized depths.

4. The Corps will coordinate project dredging schedules and plans with the Service, NMFS, and CDFW with the intent of reducing and avoiding any adverse project effects to listed species and designated critical habitats to the extent feasible. In addition, a biological monitor will conduct pre-dredging, aquatic, and/or terrestrial pre-construction surveys prior to all maintenance dredging.

5. A maintenance dredging work window is proposed to follow a yearly schedule between August 1 through October 31 for the SRDWSC. A standard 2-week extension is also proposed, after concurrence with the Service and NMFS, extending dredging in the SRDWSC to November 15, on a case-by-case basis. If any extension period beyond the traditional work window is granted, fish entrainment/capture monitoring shall be increased to 24/7 monitoring as fish are more likely to be present outside of the environmental work windows.

6. If two dredgers are used in a single channel, they will not operate in the same reach to reduce the length of channel that fish are exposed to elevated turbidity. Alternatively, if two dredgers are used in the same reach, a turbidity curtain must be used downstream of each dredger to reduce the length of channel that fish are exposed to elevated turbidity.

Mr. Marshall K. Harper 12

7. All slurry pipe placement and bank stabilization activities will specifically avoid known locations containing special status species and/or designated critical and other sensitive habitats to the maximum extent feasible.

8. 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 will be removed after the area has been stabilized.

9. A Corps representative will be identified as the point of contact for any contractor who might incidentally take a listed species. This point of contact will be identified to all construction employees during an orientation regarding the potential effects on listed species. The orientation will be conducted by a qualified biologist and cover specific information on measures to prevent injury to listed species and what to do if any are found in the project area.

10. Fish entrainment/capture monitoring will be conducted for all dredging work. The

Corps and its contractors will pursue a monitoring target of 30 percent of the material dredged in accordance with the procedures, unless operating outside of the environmental work window wherein the Corps and its contractors will attempt to monitor all dredged material for fish entrainment using a cutterhead dredge and will double the monitoring conducted if using clamshell.

Hydraulic dredging measures:

1. Cutterheads will not be operated more than 3 feet above the channel bottom.

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

3. 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.

4. A drag beam or similar device will not be used to “knock down” ridges or high spots on the channel bottom.

5. The cutterhead rotation speed would be reduced as needed to reduce the potential for side casting the excavated sediment away from the suction entrance and resuspending sediment.

Mr. Marshall K. Harper 13

6. The swing speed would be reduced as needed to ensure that the dredge head does not move through the cut faster than it can hydraulically pump the sediment. Reducing swing speed reduces the volume of resuspended sediment. The goal is to swing the dredge head at a speed that allows as much of the disturbed sediment as possible to be removed with the hydraulic flow. Typical swing speeds range from 5 to 30 feet per minute.

7. Bank undercutting will be eliminated, and sediment will be removed in maximum lifts equal to 80 percent or less of the cutterhead diameter.

8. The hydraulic dredge will operate on the bottom of the channel, and the velocity of water moving toward the dredge cutterhead will be less than 1 foot per second within

9 feet of the suction pipe opening.

Mechanical dredging measures:

1. Multiple horizontal dredge cuts will be taken where a thick horizontal volume needs to be dredged to avoid overfilling the bucket and causing spillage. Once the clamshell bucket reaches the target depth, it will be fully closed before the dredge operator begins to raise it to the surface of the water column. This method, coupled with the use of a mechanical cable arm environmental clamshell bucket, minimizes the potential for generating turbidity in the water column. Once out of the water, the clamshell bucket will place dredged sediment directly into the scow. Sediment will not be released from the bucket until it is fully inside the scow. Within the scow, dredged sediment will pass through a 12-inch-by-12-inch grid to prevent any solid debris or artificial objects from entering the scow. Solid debris and artificial objects trapped on the grid will be removed and brought to an approved waste disposal site.

The bucket will be held open over the grid within the scow until all the sediment and water has drained from within it to minimize the potential for resuspension of the sediment in the water column.

2. The load line on disposal barges used for mechanical dredging will be predetermined based on channel conditions, and the barge will not be filled above this predetermined level. Under no circumstance will scows be loaded to more than 90 percent capacity.

3. Before each disposal barge is transported to a placement site, the dredging contractor and a site inspector must certify that it is filled correctly. Scows will be inspected to ensure no loss of sediment during loading and transport.

4. If turbidity levels reach a value that represents 75 percent of the relevant allowable limit as identified in the MOU for any reason, the Corps’ contractor will immediately slow the dredge rate by 50 percent to prevent turbidity levels from increasing further

(i.e., if the cycle time for the bucket to descend, collect material, and drop that material in the scow is 30 seconds when the violation occurs, the revised cycle time should be 45 seconds until levels return to below 75 percent relevant allowable limits).

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5. If turbidity levels reach a value that represents 90 percent of the relevant allowable limit as identified in the MOU for any reason, the Corps’ contractor will deploy a type II turbidity curtain, bubble curtain, or other similar measure to prevent the plume from migrating away from the dredge site. The curtain shall remain in place until levels have returned to below 75 percent relevant allowable limits. The cycle time will be increased as needed to reduce the velocity of the ascending loaded bucket through the water column, which reduces potential to wash sediment from the bucket.

Giant Garter Snake

Biological surveys for the presence of GGS would be conducted by approved biologists prior to use at each DMPS, placement of bank slope protection, and road maintenance work at S-31.

Additional measures, as directed by the Service, would be taken as extra precaution during the dormant period, including but not limited to:

1. Since maintenance dredging and bank protection work near potential GGS habitat(s) may occur beyond the GGS work-window limit between October 1 and up to

November 15, 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 feet of suitable GGS habitat including suitable aestivation habitats such as rock outcroppings or small animal burrows.

2. Dredging and construction personnel will participate in a Service-approved worker environmental awareness training to instruct workers to recognize and avoid GGS and their habitat(s). 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.

3. 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.

4. A Service-approved biological monitor will be onsite at the beginning of each construction day for new DMPS preparation construction. The monitor would inspect the site prior to the start of each construction day to determine the presence of GGS or other sensitive species. The site inspection would include all items left onsite overnight, including equipment, vehicles, and fence lines. The inspection would also include areas within or near active soil disturbance. The monitor would then be allowed to leave the site for the day after the site and fence inspection is completed.

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5. Installation of wildlife exclusion fencing will be installed along the perimeter of the project footprint for new DMPS preparation construction to exclude GGS.

Installation specifications of the wildlife exclusion fencing comprise a 4-inch anti-climbing lip, 36-inch above-ground physical barrier, and the bottom keyed into a depth of 18 inches and backfilled with soil to prevent GGS from passing under the fence and entering the project footprint. Burying the fence will also discourage animals from burrowing under the fence providing a means for GGS to access the site. Exit ramps will be installed at regular intervals and will be accessible from ground level to allow GGS and other wildlife present on the site prior to fencing installation to escape from within the project site following installation. After installation, the Service-approved biological monitor will inspect the exclusionary fencing at the beginning of each construction day to ensure that its integrity is maintained and report any damages or compromises. Any damages or compromises to the fencing will be repaired immediately before construction continues.

6. Initiation of maintenance projects, including road maintenance, will begin between

May 1 and October 1. This is the active period for GGS and direct mortality potential is lessened because snakes are expected to actively move and avoid danger and snakes are less likely to enter an active construction site once construction has commenced.

7. Clearing shall be confined to the minimal area necessary to facilitate construction activities. Potential GGS habitat within or adjacent to the construction area will be flagged as Environmentally Sensitive Areas and avoided by all construction personnel.

8. At least 24 hours prior to containment berm construction activities, the construction area will be surveyed for GGS. Survey of the area will be repeated if a lapse of construction activity of two weeks or greater has occurred. If a snake is encountered during containment berm construction, activities will cease until appropriate corrective measures have been completed or it has been determined that the snake will not be harmed.

9. Clearing will be confined to the minimal area necessary to facilitate construction activities.

10. After the completion of construction activities, temporary fill and construction debris will be removed. Bare soil, soil-filled riprap, and levee slopes will be hydroseeded.

Temporary staging and stockpile areas would 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.” The Action

Area for this consultation encompasses all areas that may be directly or indirectly affected as a result of activities for the project and the broader area that, while outside the project footprint, Mr. Marshall K. Harper 16 may be directly or indirectly affected by vibrations, noise, lighting, or movement associated with the proposed project. For the purposes of this biological opinion, the Action Area encompasses portions of the SRDWSC, with their associated riverbanks in the Sacramento River, as well the five DMPSs within the legal California Delta (this excludes Montezuma Wetlands). This constitutes approximately 8,500 total aquatic channel acres (geospatial) of the SRDWSC identified in Figure 1. The Action Area also includes approximately 1,768 total terrestrial acres based on the information of each of the five DMPSs described in Table 1. Although the Service has determined that the Action Area includes all of the aquatic environment in the SRDWSC, we anticipate that the Corps will only operate in approximately 10 percent of the total acreage throughout a dredging season.

The Montezuma Wetlands DMPS is a beneficial reuse site that is part of the Corps’ “Long-term

Management Strategy for the Placement of Dredged Material in the San Francisco Bay Region”.

Even though this DMPS is in the Action Area for this proposed action, material placement at this site has already been addressed in biological opinions previously issued for the Montezuma

Wetlands Project dated March 21, 2001 (Service file number 1-1-99-F-12), with amendments in

2002 (Service file number 1-1-02-F-0175), in 2004 (Service file number 1-1-04-F-270), in 2010

(Service file number 81420-2008-F-1861), and in 2022 (Service File number 2022-0074267-S7-

001). All avoidance and minimization measures will be followed, including the ones proposed in this document.

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Figure 1. Overview of the proposed action showing location of the SRDWSC (dark blue) and

DMPS (red). The proposed Montezuma DMPS is denoted with a blue number.

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Analytical Framework for the Jeopardy Determination

Section 7(a)(2) of the Act requires that Federal agencies ensure that any action they authorize, fund, or carry out is not likely to jeopardize the continued existence of listed species.

“Jeopardize the continued existence of” means to engage in an action that reasonably would be expected, directly or indirectly, to reduce appreciably the likelihood of both the survival and recovery of a listed species in the wild by reducing the reproduction, numbers, or distribution of that species (50 CFR § 402.02).

The jeopardy analysis in this biological opinion considers the effects of the proposed Federal action, and any cumulative effects, on the rangewide survival and recovery of the listed species.

It relies on four components: (1) the Status of the Species, which describes the current rangewide condition of the species, the factors responsible for that condition, and its survival and recovery needs; (2) the Environmental Baseline, which analyzes the current condition of the species in the Action Area without the consequences to the listed species caused by the proposed action, the factors responsible for that condition, and the relationship of the Action Area to the survival and recovery of the species; (3) the Effects of the Action, which includes all effects that are caused by the proposed Federal action; and (4) the Cumulative Effects, which evaluates the effects of future, non-Federal activities in the Action Area on the species. The Effects of the

Action and Cumulative Effects are added to the Environmental Baseline and in light of the status of the species, the Service formulates its opinion as to whether the proposed action is likely to jeopardize the continued existence of listed species.

Analytical Framework for the Adverse Modification Determination

Section 7(a)(2) of the Act requires that Federal agencies ensure that any action they authorize, fund, or carry out is not likely to destroy or to adversely modify designated critical habitat. A final rule revising the regulatory definition of “destruction or adverse modification” (DAM) was published on August 27, 2019 (84 FR 44976). The final rule became effective on October 28, 2019. The revised definition states:

“Destruction or adverse modification means a direct or indirect alteration that appreciably diminishes the value of critical habitat as a whole for the conservation of a listed species.”

The DAM analysis in this biological opinion relies on four components: (1) the Status of Critical

Habitat, which describes the current range-wide condition of the critical habitat in terms of the key components (i.e., essential habitat features, primary constituent elements, or physical and biological features) that provide for the conservation of the listed species, the factors responsible for that condition, and the intended value of the critical habitat overall for the conservation/recovery of the listed species; (2) the Environmental Baseline, which analyzes the current condition of the critical habitat in the Action Area without the consequences to designated critical habitat caused by the proposed action, the factors responsible for that condition, and the value of the critical habitat in the Action Area for the conservation/recovery of the listed species; (3) the Effects of the Action, which determines all consequences to designated critical habitat that are caused by the proposed Federal action on the key components of critical habitat that provide for the conservation of the listed species, and how those impacts are likely to influence the conservation value of the affected critical habitat; and (4) Cumulative Effects, Mr. Marshall K. Harper 19 which evaluate the effects of future non-Federal activities that are reasonably certain to occur in the Action Area on the key components of critical habitat that provide for the conservation of the listed species and how those impacts are likely to influence the conservation value of the affected critical habitat. The Effects of the Action and Cumulative Effects are added to the Environmental

Baseline and in light of the status of critical habitat, the Service formulates its opinion as to whether the action is likely to destroy or adversely modify designated critical habitat. The

Service’s opinion evaluates whether the action is likely to impair or preclude the capacity of critical habitat in the Action Area to serve its intended conservation function to an extent that appreciably diminishes the rangewide value of critical habitat for the conservation of the listed species. The key to making that finding is understanding the value (i.e., the role) of the critical habitat in the Action Area for the conservation/recovery of the listed species based on the

Environmental Baseline analysis.

Status of Species

Delta Smelt

Species Legal Status and Life Cycle Summary

The Service proposed to list the delta smelt as threatened with proposed critical habitat on

October 3, 1991 (Service 1991). The Service listed the delta smelt as threatened on March 5, 1993…