Amendment 0001 - Exhibit B - ARCF16 USFWS and NMFS BOs - SREL_23 Dec 19.pdf

In Reply Refer to:

08ESMF00-

2014-F-0518

Ms. Alicia E Kirchner Chief, Planning Division

Sacramento Fish and Wildlife Office

2800 Cottage Way, Suite W-2605

Sacramento, California 95825-1846

U.S. Army Corps of Engineers, Sacramento District 1325 J Street Sacramento, California 95814

SEP 11 2015

Subject: Formal Consultation on the American River Common Features (AFRC) Project, Sacramento County, California

Dear Ms. Kirchner:

Tins letter is in response to the U.S. Army Corps of Engineers (Corps) April 3, 2015, request for consultation with the U.S. Pish and Wildlife Service (Service) on the proposed American River Common Features General Reevaluation Report (ARCF GRR) project in Sacramento County, California. You request was received by the Service on April 7, 2015. The Corps originally initiated consultation on June 30, 2014; however, the Service responded on July 23, 2014, with a request for additional information regarding the project description and the effects analysis the Corps had completed. The April 3, 2015, letter and biological assessment began the formal consultation period. Tlus response is provided under the authority of the Endangered Species Act of 1973, as amended (16 U.S.C. 1531 et seq.) (Act).

'I11e Federal action on which we are consulting is the ARCF GRR, which includes levee improvements and bank protection along th� Sacramento River, levee improvements along Arcade, Magpie, and Dry/Robla Creeks, widening the Sacramento Bypass and Weir, and bank protection along the lower American River. Pursuant to 50 CFR 402.120), you submitted a biological assessment for our review and requested concurrence with the findings presented therein. These findings conclude that the proposed project may affect and is not likely to adversely affect the vernal pool fairy shrimp (Branchinecta fyncht) and vernal pool tadpole shrimp (Lepidums packardt); may affect likely to adversely affect the valley elderberry longhorn beetle (Desmocems californicus dimorphus), delta smelt (H.Jpomesus transpacificus) (smelt) and its critical habitat; the giant garter snake (Thamnophis gigas);

and the yellow-billed cuckoo (Cocryi}ls americanus octidentalis) . The project is outside of critical habitat designated for tl1e valley elderberry longhorn beetle and critical habitat proposed for the yellow billed cuckoo.

TI1e Corps previously consulted with the Service on tl1e Magpie Creek Flood Control Project and on September 15, 2004 a biological opinion regarding effects to the vernal pool fairy shrimp, vernal pool tadpole shrimp, and giant garter snake (File# 1-1-04-F-0132) was provided. rfl1e project described in tl1e 2004 biological opinion is exactly tl1e same as the Magpie Creek portion of the

Ms. Alicia E. Kirchner 2 project description in the Common Features biological assessment. Because the environmental baseline for vernal pool fairy shrimp and vernal pool tadpole shrimp has not changed from the baseline that was analyzed in the 2004 biological opinion and the project description remains the same, effects to and take of vernal pool fairy shrimp and vernal pool tadpole shrimp are addressed in the September 15, 2004, biological opinion. More recent information regarding the status of the habitat along Magpie Creek for giant garter snake has changed from d1e 2004 biological opinion.

This opinion addresses those changes and any potential effects to the giant garter snake.

Seasonal wedands, which may provide suitable habitat for vernal pool fairy shrimp and vernal pool tadpole shrimp, occur in the vicinity of the Robia Creek woodland mitigation site A, however any vernal pools in this area would be avoided by these activities. TI1e Corps will implement a 250-foot buffer between vernal pools and vegetation planting. Planting activities will be done in the fall when the wedands are dry and will use best management practices to ensure that sediment does not enter the seasonal wetlands. The Service concurs that with your determination of may affect, not likely to adversely affect vernal pool fairy shrimp and vernal pool tadpole shrimp at the Robia Creek woodland mitigation site A.

This biological opinion is based on information provided in the Corps' letter requesting consultation and the biological assessment. A complete administrative record is on file at the Service's Sacramento Fish and Wildlife Office.

CONSULTATION HISTORY

September 4, 2013: The Service commented on the April2013 draft biological assessment.

April 8, 2014: The Service commented on the October 2013 draft biological assessment.

June 30, 2014: The Corps initiated section 7 consultation with the Service.

July 23, 2014: The Service sent a letter in response to the Corps initiation requesting additional information.

April 3, 2015: The Corps provided an updated biological assessment with responses to the Service's July 23, 2014, request for additional information.

August 31, 2015: The Corps provided a revised biological assessment that addressed questions the Service had regarding the project description.

BIOLOGICAL OPINION

Description of the Action

Congress directed the Corps to investigate the feasibility of reducing flood risk of the city of Sacramento. The Corps completed feasibility studies in 1991 and 1996, recommending a concrete gravity flood detention dam on the north fork of the American River at the Auburn site along with levee improvements downstream of Folsom Dam. Other plans evaluated in the report were Folsom Dam improvements and a stepped release plan for Folsom Dam releases. These additional plans also included levee improvements downstream of Folsom Dam. Congress recognized that levee improvements were "common" to all candidate plans in the report and that there was a Federal interest in participating in these "common features." Thus, the ARCF Project was authorized in the Water Resources Development Act (WillA) of 1996 and a decision on Auburn Dam was deferred

Ms. Alicia E. Kirchner to a later date. Major construction components of ARCF in the WRDA 1996 authorization included construction of seepage remediation along about 22 miles of American River levees and construction of levee strengthening and raising of 12 miles of Sacramento River levee in Natomas.

Following the 1986 flood, significant seepage was experienced on the Sacramento River from Verona (upstream end ofNatomas) at River Mile (RM) 79 to Freeport at RM 45.5. In addition, both the north and south bank of the American River from RM 0 to about RM 11.4 experienced seepage. Seepage on the Sacramento River was so extensive that Congress, soon after the 1986 flood event, funded remediation in the Sacramento Urban Levee Improvement Project (Sac Urban).

The Sac Urban Project constructed shallow seepage cutoff walls from Powerline Road in Natomas at approximately RM 64 down to Freeport.

Shortly thereafter, the Sacramento Valley experienced a flood event in 1997. Considerable seepage occurred on the Sacramento River as well as on the American River. Seepage on the American River was expected because remediation measures had yet to be constructed, but the occurrence of significant seepage on the Sacramento River in the reach remediated as part of the Sac Urban Project was alarming and confirmed that deep underseepage was also of significant concern. As a result, seepage remediation on the American River (then in the late 1990s in the design phase) would need to be designed to remediate both through- and deep underseepage.

In 1999, Congress decided not to authorize Auburn Dam, but instead authorized improvements for Folsom Dam. By doing this, improvements to levees downstream of Folsom Dam could be fine tuned to work closely with the Folsom improvements being discussed by Congress. Therefore, the ARCF project was modified by WRDA 1999 to include additional necessary features for the American River so that it could safely convey the proposed emergency release of 160,000 cubic feet per second (cfs) from Folsom Dam. Major construction components for the ARCF project in the WillA 1999 authorization include construction of seepage remediation and levee raise along four stretches of the American River, and construction of levee strengthening and raising of 5.5 miles of

Natomas Cross Canal levee in Natomas. All American River features authorized in WRDA 1996 and 1999 have been constructed or are in design analysis for construction within a year or two.

TI1e purpose of the ARCF project is to reduce the flood risk for the city of Sacramento. The following problems were identified within d1e Sacramento levee system:

• Seepage and underseepage;

• Levee erosion;

• Levee stability;

• Levee overtopping;

• Access for maintenance and flood fighting;

• Vegetation and encroachments;

• Releases from Folsom Dam;

• Floodplain management; and

• Additional upstream storage from existing reservoirs.

In order to evaluate the effects to listed species, the Corps looked at the largest foreseeable footprint. As the Corps moves into the design phase of the project, footprint changes will likely reduce the effects to listed species.

Ms. Alicia E. Kirchner 4

The project is designed to allow for the release of 160,000 cubic feet per second ( cfs) from Folsom Dam. The levees along the American River are unable to withstand these maximum flows for extended periods of time without increased risk of erosion and potential failure. The exact location where erosion will occur and to what extent erosion will occur during any given event is unknown.

Erosion within the American River Parkway will be addressed as part of the Folsom Dam Water Control Manual Update currendy under evaluation and a biological assessment is being prepared to initiate section 7 consultation with both d1e Service and National Marine Fisheries Service (NMFS).

Therefore, the effects of erosion along d1e lower American River and effects of increased Yolo Bypass flooding frequency due to changes in operations from Folsom Dam are not analyzed in this project description. This is because construction of the American River and Sacramento Bypass measures, which are dependent on releases from Folsom Dam, will not occur until after a biological opinion is received for the Water Control Manual Update. Sacramento River and East Side Tributaries measures are necessary to improve the flood risk management system in the Sacramento area regardless of the change in operation at Folsom Dam and are not dependent on Folsom Dam operations for their implementation. As a result, construction in these areas could occur regardless of the Folsom Dam Water Control Manual Update schedule.

The Corps' project involves the construction of ftx-in-place levee remediation measures to address seepage, stability, erosion, and height concerns identified for the Sacramento River and American River levees, Natomas East Main Drainage Canal (NEMDC), Arcade, Dry /Robla, and Magpie Creeks (Figure 1 ). Most height concerns along the Sacramento River will be addressed by a widening of the Sacramento Weir and Bypass to divert more flows into d1e Yolo Bypass. Due to the urban nature and proximity of existing development within the American River North and South basins the Corps is planning fix in place remediation. This would improve the flood damage reduction system to safely convey flows to a level that maximizes net benefits. Table 1 summarizes the levee problems discussed above and the proposed measure for each waterway.

Sacramento Area Flood Control Agency (SAFCA), the project's local sponsor, will complete some portions of the Federal project. SAFCA is seeking permission from the Corps pursuant to 33 USC §408 (Section 408) for alteration of the Federal levees along the NEMDC and Arcade Creek.

In addition to the proposed levee improvements measures shown in Table 1, the following measures and policies would be addressed during construction:

• The non-Federal (Department of Water Resources (DWR)) will bring the levees into compliance with the Corps' standard levee footprint using a System Wide Implementation Framework (SWIF) process. A SWIF is a plan developed by the levee sponsor(s) and accepted by d1e Corps to implement system-wide improvements to a levee system (or multiple levee systems within a watershed) to address system-wide issues, including correction of unacceptable inspection items, in a prioritized way to optimize flood risk reduction. The standard levee footprint consists of a 20 foot crown width, 3:1 waterside

Legend Improvements

-�..eveeeroau EZl llyp:JS! & We'r Widening

� ._.... • Erosion

� S1ro:IIT8 • Height

D .. . i CoootyBolnla!Y • 5eepoge/Stabilty

MilO Extent ::'a !...lcri»n,.nt

I'., . . (!.,., ''"'I lllfiiJ'til l J • \

•,{ I

Figure 1. American River Common Features Project Area

AMERICAN RIVER COIIIIOII FEATURES GRR

SACRAIIEIITO, CAUFORIIIA

AMERICAN RIVER

LEVEE IMPROVEMENTS

ALTERNATIVE 2

U.S. ARMY CORPS OF ENGINEERS

SACRAIIEIITO DISTRICT

Ms. Alicia E. Kirchner 6

T bl 1 R a e . eme di . b w anon ,y aterway.

Waterway Seepage Measures Stability Measures Erosion Overtopping

Protection Measures Measures

American Rivert --- --- Bank Protection, --- Launchable Rock Trench (31,000 linear feet) Sacramento River Cutoff Wall Cutoff Wall Bank Protection Sacramento

(50,300 linear (50,300 linear (50,300 linear Bypass and Weir feet) feet) feet) Widening, Levee

Raise (1 ,500 feet) NEMDC Cutoff Wall Cutoff Wall --- Flood wall

(6,000 linear feet) (15,600 linear feet)

Arcade Creek Cutoff Wall Cutoff Wall --- Flood wall (22,000 linear (22,000 linear feet) feet) Dry/Robla --- --- --- Flood wall Creeks (2,500 linear feet) Magpie Creek2 --- --- --- Floodwall, Levee

Raise

1Amencan River seepage, stability, and overtopping measures were addressed in a previous construction project.

2In addition to the floodwall, Magpie Creek will include construction of a new levee (3, 100 linear feet) along Raley Boulevard south of the creek, and construction of a detention basin on both sides of Raley Boulevard (19 acres). In addition, some improvements would need to occur on Raley Boulevard, including widening of the Magpie Creek Bridge, raising the elevation of the roadway, and removing the Don Julio Creek culvert.

slope and 2:1 landside slope, when possible. If the 3:1 waterside slope is not possible, then a minimum 2:1 waterside slope would be established instead.

• Engineering Technical Letter 1110-2-583 (ETL) vegetation compliance would occur under a SWIF by the local maintaining agency (LMA). The intent of the SWIF is to collaboratively work with the resource agencies and levee sponsors to transition existing levees to Corps standards while maintaining Public Law (PL) 84-99 rehabilitation assistance and adhering to the Act and other environmental laws. The SWIF is a two-step process completed by the applicant that is composed of a letter of intent, which is followed by submission of a SWIF plan. The SWIF process allows eligible local sponsors to implement levee improvements in a prioritized "worst first" way to optimize the achievement of risk reduction. The Corps acknowledges that implementing system-wide improvements will need to be done within a collaborative intergovernmental framework and that it will take time to develop and implement improvements in complex situations. Challenges including ensuring that both environmental and levee safety considerations are adequately served.

• The vegetation requirements for the SWIF include a 15-foot waterside, landside, and vertical vegetation-free zone. Trees that pose an unacceptable risk to levee integrity will be removed and the root balls and roots will be remediated. Trees that do not pose a threat will not be removed. Vegetation on the land side slope would only be removed within the construction footprint (up to 1/2 levee degrade) and the remaining vegetation would be dealt with under the SWIF process.

• Utility encroachments will be brought into compliance with Corps policy. Utilities that penetrate the levee would be removed and replaced with one of two fixes: (1) a surface line over the levee prism, or (2) a through-levee line equipped with positive closure devices.

• Private encroachments shall be removed by the non-Federal sponsor prior to construction.

• The Sacramento District of the Corps will pursue a vegetation variance which will allow vegetation on the lower 1/2 of the levee slope to 15 feet waterward of the waterside levee toe to remain in place. The Sacramento District has conducted an evaluation which examined the safety, structural integrity, and functionality of the levees that will be retained and not compromised if a tree were to fall and result in scouring of the root ball area. The results show that the tree fall and scour did not significantly affect levee performance, and the levee meets Corps seepage and slope stability criteria assuming the entire project is constructed.

American River

Levees along the American River require improvements to address erosion. The proposed measures for tl1ese levees consist of waterside armoring to prevent erosion to the river bank and levee, which could potentially undermine the levee foundation. There are two measures proposed for the American River levees: (1) a maximum of 31 ,000 linear feet (LF) of bank protection, and (2) a maximum of 65 acres/45,000 LF of launchable rock trench. Both of these measures are described in detail in the subsections below. These numbers are maximized because there is some overlap identified to account for the uncertainty of site-specific conditions. For example, for some reaches botl1 bank protection and launchable rock trench impacts were estimated even though both measures will not be constructed in the same reach.

Bank Protection

This measure consists of placing rock revetment on the river's bank to prevent erosion. It entails installing revetment along the stream bank based on site-specific analysis (Figure 2).

When necessary, the eroded portion of the bank will be filled and compacted prior to the rock placement. The sites will be prepared by clearing and stripping of loose material and understory growth prior to construction. In most cases, large vegetation will be permitted to remain at tl1ese sites. Temporary acce�s ramps will be constructed, if needed, using imported borrow material that would be trucked on site.

The placement of rock onto the bank will occur from a land based staging area using long reach excavators and loader. The loader brings rock from a permitted source and stockpiles it near the levee in the construction area. The excavator then moves the rock from the stockpile to the waterside of the levee.

111e revetment will be placed on the existing bank at a slope varying from 2V:1H to 3V:1H depending on site specific conditions. After revetment placement has been completed, a planting berm will be constructed in the rock to allow for revegetation of the site. The planting berm varies in width from 5 to 15 feet. In all cases the planting will occur outside tl1c vegetation free zone as required by the ETL.

'?Winter/Spring \] Summer/Fall

Wetland Bench

Zone 28 Riparian

Bench

Zone 2A Zone 1 Upper Riparian Vegetation

Free

Figure 2. Bank Protection with Planting Bench.

Launchable Rock Trench

Top of Levee

For the purposes of this project description, it is assumed that 65 acres of the lower American River will have a launchable rock trench ftx. The remainder will be the bank protection described above. This measure includes construction of a launchable rock filled trench, designed to deploy once erosion has removed the bank material beneath it (Figure 3).

All launchable rock trenches will be constructed outside of the natural river channel. The vegetation will be removed from the footprint of the trench and the levee slope prior to excavation of the trench. The trench configuration will include a 2:1 landside slope and 1:1 waterside slope and will be excavated at the toe of the existing levee. All soil removed during trench excavation will be stockpiled for potential reuse. The bottom of the trench will be constructed close to the summer mean water surface elevation in order to reduce the rock launching distance and amount of rock required.

After excavation, the trench will be ftlled with revetment that will be imported from an offsite commercial location. After rock placement the trench will be covered with a minimum of 3 feet of the stockpiled soil for a planting berm. Rock placed on the levee slope will be covered with 2 feet of stockpiled soil. All disturbed areas will be reseeded with native grasses and small shrubs where appropriate. Trees and shrubs could be permitted on the trench if planted outside the specifted vegetation free zone as required by the ETL.

Sacramento River

Levees along the Sacramento River require improvements to address seepage, stability, and erosion.

About 50,300 LF of bank protection and cutoff wall or slope stability work is proposed for the Sacramento River. In addition, these levees require a total of one mile of intermittent height improvements in order to convey additional flows that exceed current design levels.

. Ms. Alicia E. Kirchner

Waterside

Hydroseeded Surface J

American River Launchable Trench Scenario

American River Bank Protection Scenario

Existing Cutoff Wall

Exfstlng Cutoff Wall

Figure 3. Launchable Rock Trench and Bank Protection.

Landside

15'

- Extent of Vegetation Removal

SWIF

Where the existing levee does not meet tht: levee design requirements, as discussed above, slope flattening, crown widening, and/ or a minimal amount of levee raise is required. This improvement measure addresses problems with slope stability, geometry, height and levee crest access and maintenance. To begin levee embankment grading, loose material and vegetation understory will be cleared, grubbed, stripped, and where necessary, portions of the existing embankment will be excavated to allow for bench cuts and keyways to tie in additional embankment fill. Excavated and borrow material (from nearby borrow sites) will be stockpiled at staging areas. Haul trucks and front end loaders will bring borrow materials to the site, which will then be spread evenly and compacted according to levee design plans.

The levee will be raised about 1 to 2 feet resulting in the levee footprint extending out a maximum of 5 feet on the landside from tht: existing levee. The levee crown patrol road will be re-established at the completion of construction.

Cutoff Walls

To address seepage concerns, a cutoff wall will be constructed through the levee crown.

111e cutoff wall will be installed by one of two methods: (1) conventional open trench cutoff walls, or (2) deep soil mixing (DSM) cutoff walls. The method of cutoff wall selected for each reach will depend on the depth of the cutoff wall needed to address the seepage. The open trench method can be used to install a cutoff wall to a depth of about 85 feet. For cutoff walls of greater depth the DSM method will be utilized.

Ms. Alicia E. Kirchner 10

Prior to any cutoff wall construction method, the construction site and any staging areas will be cleared, grubbed, and stripped. The levee crown will be degraded up to half the levee height to create a large enough working platform (about 30 feet) and to reduce the risk of hydraulically fracturing the levee embankment from the insertion of slurry fluids. This method of slurry wall installation will also reduce the risk of slurry mixture following seepage paths and leaking into the river or into landside properties.

Open Trench CutoffWall

Under the open trench method, a trench about 3 feet wide will be excavated at the top of levee centerline and into the subsurface materials up to 85 feet deep with a long boom excavator. As the trench is excavated, it is filled with low density temporary bentonite water slurry to prevent cave in. The soil from the excavated trench is mixed nearby with hydrated bentonite, and in some applications cement. The soil bentonite mixture is backfilled into the trench, displacing the temporary slurry. Once the slurry was hardened, it will be capped and the levee embankment will be reconstructed with impervious or semi-impervious soil.

DSM CutoffWall

The DSM method involves a crane supported set of two to four mixing augers used to drill through the levee crown and subsurface to a maximum depth of about 140 feet. As the augers are inserted and withdrawn, a cement bentonite grout will be injected through the augers and mixed with the native soils. An overlapping series of mixed columns will be drilled to create a continuous seepage cutoff barrier. A degrade of up to one half the levee height will be required for construction of the DSM wall. For both methods, once the slurry has hardened it will be capped and the levee embankment will be reconstructed with impervious or semi-impervious soil.

Bank Protection

Proposed bank protection along the Sacramento River will address erosion concerns.

Studies have shown that the Sacramento River levees have a medium to high risk of breach due to erosion. Bank protection will be addressed by standard bank protection with planting berm. The standard bank protection measure for the Sacramento River consists of placing rock protection on the bank to prevent erosion. This measure entails filling the eroded portion of the bank, where necessary, and installing revetment along the waterside levee slope and streambank from streambed to a height determined by site-specific analysis. Large trees on the lower half of the waterside slope will be protected in place to retain shaded riverine aquatic (SRA) habitat. The sites will be prepared by removing vegetation along the levee slopes at either end of the site for construction of a temporary access ramp, if needed.

The ramp will then be constructed using imported commercial borrow material that will be trucked on site.

The placement of rock onto the levee slope will occur from atop the levee and/ or from the waterside by means of barges. Rock required within the channel, both below and slightly above the water line at the time of placement, will be placed by an excavator located on a barge. Construction will require two barges: one barge would carry the excavator, while the other barge will hold the stockpile of rock to be placed on the channel slopes. Rock required on the upper portions of the slopes will be placed by an excavator located on top of the levee. Rock placement from atop the levee will require one excavator and one loader for each potential placement site. The loader brings the rock from a permitted source and stockpiles it near the levee in the construction area. The excavator then moves the rock from the stockpile to the waterside of the levee.

The revetment will be placed via the methods discussed above on existing bank at a slope varying from 2V:1I-I to 3V:1H depending on site specific conditions. After revetment placement has been completed, a small planting berm will be constructed in the rock to allow for some revegetation of the site.

Natomas East Main Drain Canal

The east levee of the NEMDC requires 6,000 LF of improvements to address seepage and stability at locations where historic creeks had intersected the current levee alignment. A cutoff wall will be constructed at this location to address the seepage and stability problems. The cutoff wall will be constructed by one of the methods described in the Sacramento River section above. SAFCA is proposing to construct 1, 700 LF of cutoff wall beginning just south of the confluence of Arcade Creek and extending south along the NElviDC. The Corps will construct the remaining 4,300 LF of cutoff wall.

Arcade Creek

'l11e Arcade Creek levees require improvements to address seepage, slope stability, and overtopping when the event exceeds the current design. A centerline cutoff wall will be constructed to address seepage along 22,000 LF of the Arcade Creek levees. Levees from Rio Linda Boulevard to Marysville Boulevard will have a cutoff wall constructed at the waterside toe of the levee.

Construction of the waterside toe cutoff wall will require constructing a work bench along the toe of the levee. Excavation for the bench will extend deep enough below existing grade to remove organic material and soft, unsuitable foundation soils. Bench excavation will also extend into the existing waterside slope of d1e levee as needed. Riprap will be placed on the waterside benches after construction of the waterside toe cutoff wall. Some portions of the Arcade Creek north levee will require more substantial excavation and reconstruction of the waterside slope to provide a low permeable seepage levee slope barrier. Bench fill material will be integrated with the slope reconstruction fill to provide an integral seepage barrier with the cutoff wall over the full height of the levee slope. A small section of levee will have a sheet pile cutoff wall at the centerline of the levee, rad1er than the waterside toe cutoff wall.

'l11ere is a ditch adjacent to the north levee at the landside toe which provides a shortened seepage path, and could affect the stability of the levee. The ditch will be replaced with a conduit or box culvert and then backfilled. This will lengthen the seepage path and improve the stability of the levee. Additionally, pressure relief wells will be installed along the landside toe of the levee along the north levee west of Norwood Avenue.

The majority of the Arcade Creek levees have existing floodwalls, however there remains a height issue in this reach. A 1 to 4-foot floodwall will allow the levees to pass flood events greater than the current design level. The floodwall will be placed on the waterside hinge point of the levee and will be designed to disturb a minimal amount of waterside slope and levee crown for construction. The waterside slope will be re-established to its existing slope and the levee crown will grade away from the wall and be surfaced with aggregate base.

Ms. Alicia E. Kirchner 12

Dry and Robia Creeks

The Dry and Robla Creeks levees require improvements to address overtopping when flood events exceed the design level. Height improvements will be made with a new floodwall constructed to a height of 4 to 6 feet along 2,500 LF of the south levee. TI1e floodwall will be placed at the waterside hinge point of the levee and will be designed to disturb a minimal amount of waterside slope and levee crown for construction. Construction of the floodwall will be consistent with the description for Arcade Creek above. The waterside slope will be re-established to its existing slope and the levee crown will grade away from the wall and be surfaced with aggregate base.

Magpie Creek Diversion Canal

The Magpie Creek Diversion Canal project description is the same as was described in the September 15, 2004 biological opinion.

Sacramento Weir and Bypass

The Sacramento Weir was completed in 1916. It is the only weir in the Sacramento River Flood Control Project that is manually operated; all others overflow by gravity on their own. It is located along the right bank of the Sacramento River about 4 miles upstream of the Tower Bridge, and about 2 miles upstream from the confluence with the American River. Its primary purpose is to protect the city of Sacramento from excessive flood stages in the Sacramento River channel downstream of the American River. The weir limits flood stages (water surface elevations) in the Sacramento River to project design levels through the Sacramento/West Sacramento area.

Downstream of the Sacramento Weir, the design flood capacity of the American River is 5,000 cfs higher than that of the Sacramento River. Flows from the American River channel during a major flood event often exceed the capacity of the Sacramento River downstream of the confluence.

When this occurs, floodwaters flow upstream from the mouth of the American River to the Sacramento Weir.

The project design capacity of the weir is 112,000 cfs. It is currently 1,920 feet long and consists of 48 gates to divert floodwaters to the west through the mile-long Sacramento Bypass to the Yolo Bypass. Each gate has 38 vertical wooden plank "needles" ( 4 inches thick by 1 foot wide by 6 feet long).

Though the weir crest elevation is 24.75 feet, the weir gates are not opened until the river reaches

27.5 feet at the I Street gage with a forecast to continue rising. This gage is about 1,000 feet upstream from the I Street Bridge and about 3,500 feet upstream from tl1e mouth of the American River. The number of gates to be opened is determined by the National Weather Service/DWR river forecasting team to meet either of two criteria: (1) to prevent the stage at the I Street gage from exceeding 29 feet, or (2) to hold the stage at the downstream end of the weir to 27.5 feet (DWR 201 0). The weir gates are then closed as rapidly as practicable once the stage at the weir drops below 25 feet. This provides "flushing" flows to re-suspend sediment deposited in the Sacramento River between the Sacramento Weir and the American River during tl1e low flow periods when the weir is open during the peak of tl1e flood event (DWR 2010).

The Sacramento Weir and Bypass will be expanded to roughly twice their current width to accommodate increased bypass flows. The existing north levee of the Sacramento Bypass will be degraded and a new levee would be constructed 1,500 feet to the nortl1. The existing Sacramento Weir will be expanded to match the wider bypass. At this time, it is not known whether the new segment of weir will be constructed consistent with tl1e 1916 design described above, or whether it

Ms. Alicia E. Kirchner 13 will be designed to be a gravity-type weir. The new north levee of the bypass will be designed to be consistent with the existing Sacramento Bypass north levee; however, it will also include a 300-foot wide seepage be1m on the landside with a system of relief wells. A hazardous, toxic, and radiological waste site near the existing north levee will be remediated by the non-Federal sponsor prior to construction.

Operation of the new segment of the Sacramento Weir will occur during high water situations only, when the American River flows exceed 115,000 cfs. The existing Sacramento Weir will be operating at the pre-existing conditions described above. There are not expected to be any water quality impacts, though this has not been specifically modeled. The approximate change in water diversions, which are shown in Table 2, will vary based on the size of the flood event. The frequency of water diversion is expected to be the same, dependent on the stream gage at the I Street Bridge reaching 27.5 feet.

The widened portion of the Sacramento \Vcir will only be operated when the release from Folsom Dam is above 115,000 cfs. With the Folsom Dam improvements in place, releases from Folsom Dam will be above 115,000 cfs for flood events greater than the 1 00-year event. Therefore, for events up to and including the 1 00-year event, only the existing weir will be operated per the criteria previously established. For events greater than the 1 00-year event, when the release from Folsom Dam will go above 115,000 cfs, d1e new weir will be opened. Therefore, for events up to the 100-year event there will be no change in flow conditions in the Sacramento and Yolo Bypasses.

T bl 2 C a e ompanson o flO 100 -, -,an d 200 -year F requency Fl d v . ows un er anous c d" on ttl ons 10-Year Event Existing Condition Future Without Project Future With Project

Condition Condition American River 43,000 cfs 72,000 cfs 72,000 cfs Sacramento Bypass 50,000 cfs 66,000 cfs 66,000 cfs Yolo Bypass below 270,000 cfs 296,000 cfs 296,000 cfs Sacramento Bypass

100-Year Event Existing Condition Future Without Project Future With Project Condition Condition

American River 145,000 cfs 115,000 cfs 115,000 cfs Sacramento Bypass 131,000 cfs 115,000 cfs 115,000 cfs Yolo Bypass below 555,000 cfs 535,000 cfs 535,000 cfs Sacramento Bypass 200-Year Event Existing Condition Future Without Project Future With Project

Condition Condition American River 320,000 cfs 160,000 cfs 160,000 cfs Sacramento Bypass 183,000 cfs 149,000 cfs 164,000 cfs Yolo Bypass below 656,000 cfs 631,000 cfs 643,000 cfs Sacramento Bypass

For the 200-year event, there will be an increase in flows in the Sacramento Bypass of about 15,000 cfs. In the Yolo Bypass, this equates to an increase of about 0.10-foot of water surface elevation.

During d1e 200-ycar event, the Yolo Bypass is already flooded from levee to levee. The addition of these flows will equate to about 0.5-foot of additional width on the Yolo Bypass levee slopes.

Ms. Alicia E. Kirchner 14

High Hazard Levee Encroachment and Vegetation Removal

The National Flood Insurance Program (NFIP) standards for levee accreditation and d1e State's ULDC both require removal or modification of encroachments that pose an unacceptably high risk to the performance and safety of a levee either by undermining its structural integrity or by interfering with necessary inspection, operation, and maintenance activities. To address tlus requirement, SAFCA has identified and evaluated all of d1e encroachments in the NEMDC, Robla Creek, and Arcade Creek area. Each of these encroachments has been evaluated and based on this evaluation the encroachments have been classified as either:

• High-risk-poses a threat to levee integrity, removable prior to the levee being accredited;

• High-risk -impedes operation, maintenance, and inspection, removable within 3 years after the levee is accredited; or

• Low-risk - not identified as high hazard.

High-risk encroachments to be removed are limited to residential landscaping located at 10 locations along the landside of the south and north levees of Arcade Creek and along the Robla Creek south levee.

Vegetation on levees must be modified or removed if it presents an unacceptable risk to the structural integrity or impedes operation and maintenance of the levee. Eight rugh-risk trees along Arcade Creek have been identified for removal. All of the trees are either nonnative (J) or snags (1).

Five are located on the waterside of the levees. These trees are in addition to any trees that will be removed as a result of implementation of levee improvements in the Arcade Creek area.

Utility Relocation

Existing encroachments and penetrations wid1in the NEMDC and Arcade Creek have been inventoried by SAFCA. Many utilities will be avoided, however some utilities may need to be temporarily removed or relocated prior to construction. Temporary bypass pumping may be required for sanitary sewers. SAFCA and the construction contractors will coordinate with utility owners to manage the utilities in advance of construction. Disturbed utilities will be restored after construction consistent with Central Valley Flood Protection Board requirements.

Stormwater Pollution Prevention

Temporary erosion/runoff best management control measures would be implemented during construction to minimize stormwater pollution resulting from erosion and sediment migration from the construction, borrow, and staging areas. These temporary control measures may include implementing construction staging in a manner that minimizes the amount of area disturbed at any one time; secondary containment for storage of fuel and oil; and the management of stockpiles and disturbed areas by means of earth berms, diversion ditches, straw watdes, straw bales, silt fences, gravel filters, mulching, revegetation, and temporary covers as appropriate. Erosion and stormwater pollution control measures will be consistent with National Pollutant Discharge Elimination System (NPDES) permit requirements and included in a Stormwater Pollution Prevention Plan (SWPPP).

After completion of construction activities, the temporary facilities (construction trailers and batch plants) will be removed and the site would be restored to pre-project conditions. Site restoration activities for areas disturbed by construction activities, including borrow areas and staging areas, will

Ms. Alicia E. Kirchner 15 include a combination of regrading, reseeding, constructing permanent diversion ditches, using straw wattles and bales, and applying straw mulch and other measures deemed appropriate.

Borrow Sites, Haul Routes, and Staging Areas

Borrow Sites - It is estimated that a maximum of 1 million cubic yards (cy) of borrow material will be needed to construct the project. Detailed studies of the borrow needs have not been completed.

Actual volumes exported from any single borrow site will be adjusted to match demands for fill.

Borrow sites will be selected that avoid effects to endangered species or their habitat.

To identify potential locations for borrow material soil maps and land use maps were obtained for a 20-mile radius surrounding the project area. Except as discussed below for Arcade Creek and NEMDC, eventual borrow site selection will include the following criteria: avoid threatened and endangered species effects and habitat, current land use patterns, and soil types.

Excavation limits on the borrow sites will provide a minimum buffer of 50 feet from the edge of the borrow site boundary. From this setback, the slope from existing grade down to the bottom of the excavation will be no steeper than 3:1. Excavation depths from the borrow sites will be determined based on available suitable material. The borrow sites will be stripped of top material and excavated to appropriate depths. Once material is extracted, borrow sites will be returned to their existing use whenever possible, or these lands could be used to mitigate for project effects, if appropriate.

Because SAFCA has completed more detailed design and studies for work along NEMDC and Arcade Creek the borrow site has been selected. Borrow site 2 is located along the east side of the NEMDC north of where the levee repairs will occur. About 27,000 cubic yards of material will be excavated from the 5.5-acre borrow site in order to construct levee improvements along the NEMDC and Arcade Creek. Following borrow activities the site will be contoured to create about

0.5 acre of tule bench, set an elevation the will provide aquatic habitat all year, 1.0 acre of higher bench with seasonal wetlands, that will flood in the winter and spring, and 3.5 acres of native grassland.

Clean rock will be commercially acquired in order to construct the American and Sacramento River bank protection sites. For the Sacramento River, rock will be acquired from a commercial source in the Bay .Area and barged up the Sacramento River to the construction sites. Rock for the American river sites will be acquired from a commercial source within a 50-mile radius and will be hauled in trucks to tl1e construction sites.

Haul Routes - I Iaul routes will be determined during the design phase and will depend on what borrow sites and staging areas are selected. Haul routes will be selected based on existing commercial routes and levee roads. I Iaul routes will be selected that avoid effects to federally listed spec1es.

For Arcade Creek and NEMDC, haul trucks will leave borrow site 2 and use East Levee Road from tl1e borrow site down to a point just north of the existing Del Paso/Main Avenue Bridge over NEMDC. Temporary bridges crossing the NEMDC and Arcade Creek will be used to allow haul trucks to reach repair sites. Railroad car undercarriages on temporary abutment supports will be one option for temporary bridge crossings.

Staging Areas - Staging areas will be selected that do not require the removal of vegetation or habitat tl1at is used by threatened or endangered species or effect threatened or endangered species.

Four potential staging areas have been identified for improvements along Arcade Creek. All four

Ms. Alicia E. Kirchner 16 areas will require little preparation other than surface striping and temporary connection roads and ramps to the levee crown. The primary use of staging areas will be for temporary trailers, parking, and material staging. Additionally, there will need to be space to process material and an area where excavated soils and imported soils will be spread out and processed material. Importing, processing, and exporting material for levee reconstruction will be continuous activities once the work flow is established during the start of the construction season. Staging areas will be returned to pre-project conditions following construction activities unless the owner agrees to some grade raising to help dispose of excess construction soils.

Operation and Maintenance

Operation and maintenance (O&M) of the levees in the Sacramento area are the responsibility of the local maintaining agencies, including the American River Flood Control District, the DWR, and the City of Sacramento. The applicable O&M Manual for the Sacramento area levees is the Standard Operation and Maintenance Manual for the Sacramento Flood Control Project. Typical levee O&M in the Sacramento in the Sacramento area currently includes the following actions:

• Vegetation maintenance up to four times a year by mowing or applying herbicide.

• Control of burrowing rodent activity monthly by baiting with pesticide.

• Slope repair, site-specific and as needed, by re-sloping and compacting.

• Patrol road reconditioning up to once a year by placing, spreading, grading, and compacting aggregate base or substrate.

• Visual inspection at least monthly, by driving on the patrol road on the crown and maintenance roads at the base of the levee.

• Post-construction, groundwater levels will be monitored using the piezometers.

The Corps will work with local maintaining agencies to develop the maintenance activities necessary for long-term operations and maintenance. This will occur during the preconstruction engineering and design phase of the project. The Corps will evaluate if these maintenance activities will affect any Federally-listed species and reinitiate section 7 consultation if there will be adverse effects to listed species. Currently, the Corps only has a project description for activities that will affect valley elderberry longhorn beetle habitat. This is included below.

Following construction, the O&M manual for these reaches will be adjusted to reflect the vegetation variance and the SWIF plan. Under the adjusted O&M manual, large trees that are protected in place under the variance will be allowed to remain on the waterside slopes and additional vegetation will be planted on the planting benches.

Vegetation maintenance includes keeping maintenance roads clear of overhanging branches. Some of the vegetation along the levees includes elderberry shrubs. As part of long-term O&M, elderberry shrubs will be trimmed by the three levee maintenance districts. Table 3 describes tl1e maximum amount of elderberry acreage that will be trimmed each year as a result of O&M. Trimming consists of cutting overhanging branches along the levee slopes on both tl1e landside and waterside. Some shrubs may be located adjacent to the levee with branches hanging over the levee maintenance road.

Up to a third of a shrub will be trimmed in a single season. Trimming will occur between November 1 and March 15. Loss of habitat will be offset through the development of a conservation area as described in the conservation measures below. Each year the local maintaining agency will document the amount of valley elderberry longhorn beetle habitat that they have trimmed and report that number to the Corps to ensure compliance with this biological opinion. If the local maintaining agency has a need to exceed the amount of valley elderberry longhorn beetle habitat which needs to be trimmed or affected due to routine maintenance, then they will request the Corps reinitiatc consultation on this biological opinion for those actions.

Table 3. O&M b Maintainin_g_�ency Local Levee Systems Covered Annual Acreage of Total Acreage of Maintaining Trimmed Elderberry Elderberry Shrubs Agency Shrubs* Trimmed over the 50

Year Life of the Project American River Lower American River, 0.5 25 Flood Control Dry /Robia Creek, Arcade District Creek, NEMDC Maintenance Sacramento River east 0.2 10 Area 9 levee between Sutterville

Road and the Beach Lake Levee

City of Sacramento R.iver East 0. 1 5 Sacramento Levee between the confluence of the American River and Sutterville Road

*acreage based on an estimated average shrub of 0. 027 acre and no more than 1/3 of a shrub trimmed any given year.

Valley Elderberry Longhorn Beetle Habitat

Valley elderberry longhorn beetles arc closely associated witl1 elderberry shrubs. In 2011, the Corps conducted surveys and mapped all of the elderberry shrubs on the levees and 15 feet on either side of the levee. Elderberry shrubs were located along the American River and Sacramento River. The Corps counted shrub clusters and used elderberry stem counts from previous projects in the area to estimate a standard number and size of elderberry stems per shrub cluster. Tables 4 and 5 list the stem counts for shrubs along the American River and Sacramento River respectively. While shrubs exist along Arcade Creek or Magpie Creek, the Corps and SAFCA will avoid effects to the beetle by following the conservation measures below.

T bl 4 Am . a e . encan Ri ver Eld b er erry Shrub Effi ects an d C ti ompensa on

Exit No. of Elderberry Elderberry Associated Associated

Location Stems Native Native Holes Stems Ratios Plantings

Planting Ratios

> or = 1" & no 1,998 2 3,996 3,996 1 riparian < or = 3" yes 0 4 0 0 2 no 790 3 2,370 2,370 1 riparian > 3" & < 5" yes 16 6 96 192 2 no 312 4 1,248 1,248 1

Riparian > or = 5" yes 23 8 184 368 2

TOTAL 3,139 7,894 8,174

total basins or credits= 1,606.8 total acres for com_pensation 66.40

Location riparian riparian riparian

Ms. Alicia E. Kirchner 18

Table 5. Sacramento River Elderberry Shrub Effects and Compensation

Exit No. of Elderberry Elderberry Associated Associated

Stems Holes Stems Ratios Plantings Native Native

Plan� Ratios

> or = 1" & no 104 2 208 208 1

< or = 3" yes 0 4 0 0 2 no 40 3 120 120 1

> 3" & < 5" yes 1 6 6 12 2 no 16 4 64 64 1

> or = 5" yes 2 8 16 32 2

TOTAL 163 414 436

total basins or credits= 85 total acres need for compensation 3.51

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