US Army Corps of Engineers® Los Angeles District

Prado Basin Ecosystem Restoration and Water Conservation Study

APPENDIX C1: Fish and Wildlife Coordination Act Report C2: Response to CAR Recommendations This page intentionally left blank. U.S. States Department of the Interior FISH & WILDLIFE SERVICE U.S. FISH AND WILDLIFE SERVICE Ecological Services Carlsbad Fish and Wildlife Office ~ 2177 Salk Avenue, Suite 250 . ·''{/ Carlsbad, 92008 In Reply Refer to: FWS-OR-19B0097-20CPA0162-20E03380 August 19, 2020 Sent Electronically Colonel Julie A. Balten U.S. Army Corps of Engineers, Los Angeles District 915 Wilshire Boulevard, Suite 930 Los Angeles, California 90017-3409

Subject: Final Coordination Act Report for the Proposed Prado Basin Ecosystem Restoration and Water Conservation Project, Riverside County, California

Dear Colonel Balten:

The U.S. Fish and Wildlife Service (Service) has prepared this Final Coordination Act Report (Final CAR) for the U.S. Army Corps of Engineers (Corps) on the proposed Prado Basin Ecosystem Restoration and Water Conservation Project (Project) to describe ecological resources, project-area opportunities and constraints, and provide recommendations related to the conservation and enhancement of fish and wildlife resources. The proposed action would consist of water conservation and ecological enhancement activities. The Project area involves the and several tributaries upstream and downstream of the Prado Basin reservoir; it encompasses portions of Riverside County, San Bernardino County, and Orange County, California. The Corps worked with the Orange County Water District (OCWD) to complete a Draft Feasibility Report and Environmental Impact Statement/Environmental Impact Report (FR/EIS/EIR) in February 2019 for the proposed Project (Corps 2019a). The Corps is the lead Federal Agency and the OCWD is the lead agency under the California Environmental Quality Act for the FR/EIS/EIR.

INTRODUCTION

The Corps is the Federal lead agency for the proposed Project, pursuant to the National Environmental Policy Act. The proposed Project consists of two main components, water conservation and ecosystem enhancement. The “Water Conservation Plan” component would increase the allowable temporary storage for water conservation to a greater volume of water impoundment behind , and it would reduce the water flow releases from Prado Dam during flood seasons (as compared to the future without the proposed project after a temporary 5- year deviation expires in 2023).1 Water conservation is currently occurring up to elevation 505

1 While the instantaneous maximum water volume at elevation 505 feet held within Prado Basin would not effectively change with the proposed project, by making the allowable water surface elevation 505 feet on a permanent year-round basis, the volume of water held behind the dam would increase on an average daily basis or average yearly basis with all else being equal. The proposed project would make permanent a higher temporary pool Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E03380) 2

feet during the non-flood season, and is occurring up to 505 feet on a temporary basis as part of a five-year deviation during the flood season.

This water conservation change would assist OCWD in reducing overdraft of a primary groundwater aquifer downstream in Orange County, reduce reliance by OCWD on imported water, and increase OCWD’s local water supply. Implementation of the Project water conservation measure would result in a dam operation regulation modification by the Corps to accommodate a higher temporary pool impoundment in the basin behind Prado Dam during the fall and winter flood seasons. This extra impounded water would then be released from Prado Dam at a generally reduced rate (compared to current operations) that is optimal for OCWD’s groundwater recharge facilities that percolate water into aquifers associated with downstream reaches of the Santa Ana River. The “Ecosystem Restoration Plan” component of the Project would potentially enhance some functions of aquatic and riparian sites in the Project area. A combination of biological management measures would be implemented as part of the proposed Project, consisting of invasive plant management, native plantings, cowbird trapping, channel restoration, and sediment management. The Ecosystem Restoration Plan measures are partially designed to benefit the following species: Santa Ana sucker (Catostomus santaanae), least Bell’s vireo (Vireo bellii pusillus), southwestern willow flycatcher (Empidonax traillii extimus), yellow-billed cuckoo [western DPS (Coccyzus americanus)], and California gnatcatcher (Polioptila californica californica).

The Project direct footprint would be located within and near Prado Basin on the Santa Ana River where the boundaries of Orange, Riverside, and San Bernardino counties come together. Prado Dam is an earth-fill dam across the Santa Ana River near Corona in Riverside County, with the resulting impounded water creating Prado Basin reservoir. Prado Dam is located at a natural geomorphic constriction about 30.5 miles upstream from the Pacific Ocean in Lower Santa Ana River Canyon. Prado Dam’s primary purpose is flood risk management, and it is the downstream element of the Corps’ Santa Ana River flood risk management system. Prado Dam and Prado Basin also provide water storage for OCWD’s groundwater recharge operations downstream.

This Final CAR is provided in accordance with the Fish and Wildlife Coordination Act (FWCA) of 1958, as amended (48 Stat. 401; 16 U.S.C. 661 et seq.), the Endangered Species Act (ESA) of 1973, as amended (87 Stat. 884; 16 U.S.C. 1531 et seq.), and the scope of work agreed upon by the Corps and the Service. This CAR does constitute the report of the Secretary of the Interior as required by section 2(b) of the FWCA. It does not constitute a Biological Opinion (BO) under section 7 of the ESA. The purpose of this CAR is to deliver information and recommendations for use by the Corps in developing goals, objectives, alternatives, and conservation measures for the Project. The FWCA requires Federal agencies proposing water resource development projects, or involved in issuance of related permits or licenses, to consult with the Service and provide equal consideration to the conservation, rehabilitation, and enhancement of fish and

impoundment that was previously authorized for only five years (expiring 2023), with the result being the potential for a higher average inundation level overall.

Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E03380) 3

wildlife resources with other project purposes. This document constitutes the Service’s Final CAR for the Corps’ proposed Prado Basin Ecosystem Restoration and Water Conservation Project. The findings of this report are based on information provided in our 2020 BO FWS- WRIV-19B0097-20F0606, available data, the FR/EIS/EIR for the proposed Project, field investigations, past relevant BOs, and results of biological surveys. Our report addresses the proposed Project-related potential beneficial and adverse effects on fish and wildlife resources and provides recommendations for conservation of those resources.

In this Final CAR we emphasize the ecological river processes operating on floodplains and in river channels that create characteristic stream and vegetation structures that and maintain important fish and wildlife habitats on the Santa Ana River, particularly those that support sensitive species and highly productive natural communities. The Santa Ana River is a fluvial system, and fluvial systems naturally change through time. Like almost all California river systems, the Santa Ana River is presently in considerable state of additional flux as a result of substantial anthropogenic changes to water and sediment regimes and channel hydraulics.

Many aquatic and riparian ecosystems in the United States have been damaged or destroyed by anthropogenic activities, including drainage for agriculture, dewatering and altered flow regimes by dams, groundwater pumping and stream water diversions, floodplain filling/development, gravel mining, flood damage reduction measures, and other activities (Tiner 1984; Patten 1998; Graf 1999; Brinson and Malvarez 2002). Of substantial growing concern is the ongoing and increasing human demand for water for agricultural and domestic purposes, particularly in arid and semiarid regions of the West. This demand is intensifying the pressure on rivers and their adjacent riparian areas, wetlands, and groundwater systems and is threatening the functioning and long-term viability of these areas (Pringle 2000; Baron et al. 2002).

The economic and ecological importance of streams and rivers has led to significant restoration and rehabilitation efforts, in an attempt to return these systems towards a more natural and “healthy” condition (Karr and Chu 1999). The nature of these restoration activities is diverse and ranges from simple habitat/natural community improvement processes, such as the exotic plant control and planting of native riparian vegetation, to the implementation of environmental flows of water, hydrological experimentation, and ecological channel engineering (Palmer et al. 1997; Rutherfurd et al. 1998; Smokorowski et al. 1998).

FISH AND WILDLIFE COORDINATION ACT

The FWCA of 1934 included requirements that were the first formal expressions in U.S. law of a duty to minimize the negative environmental impacts of major water resource development projects and to compensate for those impacts that remained (Bean 2016). The FWCA was a response to a U.S. era of big dam building and reflected a concern for the impact of those dams, particularly on anadromous fish (Bean 2016). As originally enacted in 1934, it required consultation with the Bureau of Fisheries (as the Service was then known) prior to the construction of any dam to determine if fish ladders or other aids to migration were necessary and economically practical to minimize impacts on fish populations. It required, as well, the opportunity to use the impounded waters for hatcheries to offset impacts that could not otherwise Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E03380) 4 be avoided. The duties imposed by the FWCA were expanded by revisions to the FWCA in 1958 (Public Law 85-624), and reinforced by passage of the National Environmental Policy Act of 1969 (NEPA; Bean 2016). Under NEPA and its implementing regulations, all federal agencies have a duty to assess the impacts of the major actions they propose to undertake and to consider reasonable alternatives to reduce or eliminate those impacts (Bean 2016). Section 2 of the FWCA provide the authority to Federal action agencies to provide for the improvement and enhancement of fish and wildlife resources, as well as mitigation of damages from proposed projects (Smalley and Mueller 2004).

The Service, as the federal agency charged by Congress in the Fish and Wildlife Act of 1956 with the responsibility for management, conservation, and protection of fish and wildlife resources, routinely recommends mitigation measures to other federal agencies through the NEPA and FWCA processes (Bean 2016). Subsection 2(a) of the FWCA states that consultation between the Service and the Federal action agency is to be accomplished “with a view to the conservation of wildlife resources by preventing loss of and damage to such resources as well as providing for the development and improvement thereof.” Principally, the FWCA provides general authority for the Federal agencies who construct water-resource projects to incorporate in project construction and operation plans the needed measures for fish and wildlife conservation. The FWCA is not only concerned with compensatory measures to mitigate the loss of or damage to fish and wildlife resources; it contains the direction and authority to permit the implementation of means and measures to take advantage of opportunities for enhancement or improvement of fish and wildlife resources (Smalley and Mueller 2004). The FWCA stipulates that Federal water use projects should be planned to develop and improve/enhance fish and wildlife resources, where feasible, as well as to mitigate damages to them (United States House of Representatives 1958; McBroom 1958).

Coordination under the FWCA between the Service and the federal action agency typically culminates in a CAR detailing the results of data collection efforts and provides recommendations for the project moving forward. The results and recommendations are included in reports to Congress, authorization requests, and project planning documents. Through the FWCA procedural process involving consultation, investigation, and the reporting and consideration of findings and recommendations, the Service has the opportunity to offer and explain measures to benefit fish and wildlife resources, both in terms of mitigation of impacts and enhancement of fish and wildlife resources beyond offsetting potential project impacts (Smalley and Mueller 2004). In turn, the FWCA provides Federal action agencies the appropriate authorities to implement such recommendations as they find acceptable (Smalley and Mueller 2004). Corps public works authorizations (omnibus legislation) authorize Corps projects and programs, to which the FWCA is applicable as supplementary legislation (Smalley and Mueller 2004). Section 906 of the Water Resources Development Act of 1986 (33 U.S.C. 2283) on fish and wildlife mitigation enacted a number of provisions relating to mitigation and enhancement at Corps of Engineers projects (Smalley and Mueller 2004). Section 906(e) of that Act provided that the major provisions of Section 906 “shall be deemed to supplement the responsibility and authority of the Secretary pursuant to the Fish and Wildlife Coordination Act (16 U.S.C. 661 et seq.), and that nothing in this section is intended to affect that Act.” Other action agency laws Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E03380) 5

which are conditioned or supplemented by the FWCA include portions of the Clean Water Act, the Federal Power Act, and others (Smalley and Mueller 2004).

The FWCA directs and authorizes consultation, reporting, consideration, and installation/operation of fish and wildlife conservation features. Importantly, the authorities of the FWCA are considered to be “supplementary legislation” to the various Federal project authorizations, such as the Corps public works authorizations (Smalley and Mueller 2004); the FWCA “conditions or supplements other authorities”, requiring consideration of fish and wildlife opportunities in connection with such projects, and provides that justifiable measures for wildlife purposes shall be included in project plans (Smalley and Mueller 2004). It supplements other water development statutes2 to require consideration of the recommendations generated under the FWCA procedures. For Federal water resources development projects, the FWCA requires that fish and wildlife conservation receive equal consideration by Federal agencies with other project purposes and that such conservation be coordinated with other project features. The FWCA authorizes the Federal project implementation of these noted means and measures for both mitigating losses of fish and wildlife resources and for enhancing these resources beyond the offsetting of project effects (Smalley and Mueller 2004). The FWCA stipulates that fish and wildlife conservation, including prevention of losses (mitigation), is to be a goal of all Federal water projects and federally permitted or licensed water projects (Smalley and Mueller 2004).

PROPOSED PROJECT DESCRIPTION

The proposed Project within the FR/EIS/EIR consists of two separate plans: a water conservation plan and an ecosystem restoration plan. The water conservation plan would be implemented through a revision to the Prado Dam Water Control Plan (WCP). The ecosystem measures would be implemented beginning in the year 2021 and some related measure activities would extend through year 2071. Water conservation and restoration elements of the proposed Project are expected by the Corps to remain in place, functioning and continuing to provide benefits, beyond this period of analysis. The proposed ecosystem restoration measures would be implemented within four different focal areas: 1) Santa Ana River Mainstem Upstream focal area (SARM Upstream), 2) Santa Ana River Mainstem Downstream focal area (SARM Downstream), 3) Chino Creek focal area, and 4) Mill Creek focal area. The ecosystems measures are a stand-alone aspect of the proposed Project and are not intended by the Corps or OCWD to offset impacts incurred through the proposed Water Conservation Plan.

Water Conservation Plan

Prado Dam was built in 1941, just downstream of the confluences of Chino, Mill, and Temescal Creeks with the Santa Ana River. The dam’s primary purpose is flood risk management for the Santa Ana River Watershed downstream of the dam. Its secondary purpose is water conservation. Dam operations for water conservation purposes retain “excess water” in Prado Basin behind the dam for regulated release, which in turn allows OCWD to capture and percolate the slowed water discharge from the Dam in downstream groundwater spreading basins.

2 This includes portions of the Clean Water Act [Zabel v. Tabb, 430 F2d 199 (5th Cir. 1970) cert. denied 401 U.S. 910 (1972)]. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E03380) 6

Previous water control/conservation plans and associated impact minimization measures were analyzed in four BOs in 1993, 1995, 2000, and 2002 (1-6-93-F-7; 1-6-95-F-28; 1-6-99-F-75; and FWS-WRIV-2102.3, respectively). According to the Corps, water conservation is implemented in a manner that does not affect Prado Dam’s primary purpose of flood risk management.

The Corps is proposing to increase the water conservation at Prado Dam by increasing the maximum allowable storage for water conservation during the flood season, as identified in the 2003 Interim Water Control Plan (IWCP), to increase water conservation benefits for OCWD. The WCP is the basic guidance on how the water impounded behind the dam is to be regulated. It is a critical component of the Water Control Manual (WCM).3 The 2003 IWCP contains an outdated description of the operational conditions as it was prepared prior modifications for the Santa Ana River Project (SARP) currently in place. Construction of the SARP is not yet completed by the Corps, as the Prado Dam spillway structure still needs to be modified. Once the Water Conservation Plan is approved by the Corps, the Corps would incorporate those changes into the new WCP for operational decisions. The Corps has indicated that an updated WCM for Prado Dam would be produced when they are closer to initiation of construction to raise the Prado Dam spillway, in conjunction with the SARP.

The Corps proposes to increase the flood season (October 1 to February 28/29) buffer pool maximum water surface elevation (WSE) in Prado Basin from 498 ft. to 505 ft. WSE NGVD 19294 for controlled release to OCWD’s groundwater recharge facilities. The current water conservation provisions in the WCP allows retention of water to 498 ft. during flood season (October through February), and to 505 ft. during non-flood season (March through September). However, the proposed water conservation storage is already being implemented on a temporary basis, as provided for in the 5-year deviation. Therefore, the proposed change would allow a maximum buffer pool up to a water elevation of 505 ft. year-round. Additionally, during the non- flood season (March 1 to September 30), OCWD is requesting that the average discharge rate from Prado Dam be reduced from an average 500 cubic ft. per second (cfs) to 350 cfs for purposes of water conservation through maximizing groundwater recharge at their facilities year- round.

The proposed change to increase water conservation at Prado Dam would further enable OCWD to meet its goals for water conservation. In coordination with OCWD, the Corps would continue to implement controlled water releases from the buffer pool at rates consistent with the capacity of OCWD’s downstream groundwater recharge facilities (noted above) during the flood season. The proposed increase in the maximum elevation of the buffer pool during the flood season would provide approximately 10,000 acre-ft. (AF) of additional temporary storm water capture capacity. Modeling indicates that increasing the buffer pool maximum elevation to 505 ft. would, on average, result in an opportunity for OCWD to capture and recharge approximately 6,000 AF

3 The WCM includes background information, project authorization, physical features, data collection, hydrology and hydraulics, etc. A revised WCP can exist outside of an existing WCM. Updating WCMs can be a lot of effort and can trigger additional analyses or environmental coverage; a revised WCP doesn't directly require a revised WCM. 4 The National Geodetic Vertical Datum of 1929 (NGVD 29) is a sea level vertical control datum in the United States. All future elevation references within this document use this geodetic datum. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E03380) 7

of additional water per year. The Corps updated WCP would follow the operations shown in Table 1.

If the WSE exceeds or threatens to exceed 505 ft. due to increased inflow from a precipitation event, Corps Reservoir Operation Center (ROC) staff will seek to lower the WSE in Prado Basin to elevation 505 ft. as promptly as possible, matching outflow with inflow up to 5,000 cfs. The ROC will evaluate what rate of discharge will be required to either prevent inundation above elevation 505, or the appropriate maximum flood risk management discharge that will be needed to avoid a large pool and limit the duration of inundation impacts. Historically, it is not uncommon for the pool elevation to exceed elevation 505 during the flood season; the pool exceeds this elevation during the non-flood season only rarely.

The Project measure would include monitoring the health of riparian natural communities above and below 505 ft. in elevation to assess potential effects from water conservation on habitats within the Prado Basin. OCWD has an ongoing habitat monitoring program associated with existing water conservation and associated reduced outflows from Prado Dam. A combination of visual observations, photo monitoring, and Corps reservoir data would be used to detect changes in habitat distribution or function associated with the proposed changes to water conservation. To determine if riparian habitats need to be replaced, a threshold of 30 percent loss of cover within the understory over a two-season period has been established by the Project as the threshold for the replacement of vegetation. This would provide time to determine if the riparian natural communities are showing signs of recovery or degrading. For example, OCWD will monitor habitats that were inundated for more than 10 days in both 2019 and 2020 to see if at least 30 percent cover does not recover by late spring of 2022. OCWD would continue this monitoring program under the proposed measure to identify any long-term effects to native habitats and determine if steps need to be taken to mitigate those effects. The approach to vegetation monitoring is expected to evolve over time, based on a review of the ongoing results of monitoring, potential impacts identified associated with water conservation, and differences year to year in water conservation and flood risk management operations. Results from monitoring would be coordinated with the Corps and Service, as specified in Section 4.4.1 of the 2018 Biological Assessment. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 8

Table 1. A Simplification and Summary of the Expected Dam Operations Based on Water Control Plan. WSE [Water Surface Elevation] 470.0 - 490.0 (Debris Pool) (Release Range: 0 - 600 cfs)

A debris pool is allowed to form in order to prevent floating debris from being drawn into the outlet works. Water within the debris pool is released at rates that equal OCWD’s capability to recharge the groundwater without loss to the Pacific Ocean.

WSE 490.0 - 505.0 (Buffer Pool) (Typical Release Range 200-5,000 cfs)*

Operations are generally performed for water conservation. Water conservation releases are coordinated with OCWD, which typically ranges from 200 cfs to 600 cfs, normally matching OCWD’s groundwater recharge capacity, subject to minimum releases. If required for flood risk management, controlled releases of up to 5,000 cfs may occur. The release magnitude is determined by evaluating latest weather forecast and current conditions of the project status (i.e., pool elevation, observed inflow, and any downstream channel restrictions), with the goal of returning the pool to or near WSE 505. The minimum running average release is 350 cfs during the non-flood season (March 1 through September 30) when the water surface elevation is at or above 498 feet. (Note: a minimum release of 200 cfs is required during the Winter Flood Season [October 1 to February 28] except for temporary release cutbacks to facilitate OCWD reconstruction of in-stream diversion dikes. Releases greater than 500 cfs can damage OCWD's in-channel sand diversion dikes.) Existing Spillway and Incomplete Downstream Channel Existing Spillway and Completed Downstream Channel Structure Modifications Structure Modifications

WSE 505.0 - 520.0* WSE 505.0 - 520.0*

The release magnitude will depend on storm and runoff conditions, as well The release magnitude will depend on storm and runoff conditions, as well as as conditions of the reservoir and channels as to how the flood risk conditions of the reservoir and channels in the Santa Ana River watershed, as management operational objectives of the dam can best be met. The maximum reservoir to how flood risk management operational objectives can best be met. The release may be up to 5,000 cfs, unless a higher release is warranted. If maximum reservoir release may be between 12,000 cfs and 15,000 cfs, unless necessary, a maximum of 10,000 cfs may be made. A minimum of 350 cfs a higher release is warranted. The maximum discharge capacity is up to will be released during the non-flood season (March 1 to September 30). 30,000 cfs. A minimum of 350 cfs will be released during the non- flood season (March 1 to September 30).

WSE 520.0 - 543.0 WSE 520.0 - 543.0

The resulting maximum reservoir release will depend on storm and runoff The release rate may be between 12,000 and 30,000 cfs. The final water conditions, as well as conditions of the reservoir and channels in the Santa control plan does not call for the release rate of 30,000 cfs until WSE Ana River watershed. The outlet works currently in place can discharge up reaches elevation 540; however, if necessary, discharge up to 30,000 cfs to 30,000 cfs, as necessary, to avoid or limit the duration of spillway flow may be made. This maximum discharge is maintained in effort to avoid or occurrence, for dam safety. limit the duration of spillway flow occurrence, for dam safety.

* During construction of the remaining components of the SARP in Reach 9, a discharge may be limited to 800 cfs or less to protect temporary work areas and structures until this project is completed; the target date of completion is the end of the 2022 calendar year.

WATER CONSERVATION ELEVATION ABOV E SEA L EVEL PRADO DAM

...... Olm!Cse .et,R•!ls!Y.... ' ·" ." "·1

TOTAL CAPACITY 170,000 acre feet

20,000 acre feet

ater percolation from basins RESERVOIR AREA

Figure 1. Schematic representation of Prado Dam water conservation elevation for stormwater storage and capture (Corps 2019b).

Sediment Removal Associated with Water Conservation

In conjunction with the Water Conservation Plan, OCWD and the Corps propose to perform two sediment removal events along the Santa Ana River upstream of Prado Dam. In each event, 125,000 cubic yards (yd3) of sediment would be removed from a reach of the Santa Ana River just upstream of Prado Basin, for a total removal of about 250,000 yd3 of sediment excavated and placed in a sediment storage area. This action is intended to address additional sediment accumulation that would occur specifically due to the proposed water conservation operations over the 50-year period of analysis, based on analyses performed by Scheevel Engineering (2015).

Since Prado Dam was constructed, the Corps estimates that more than 25,000 AF of water conservation/storage volume has been lost below 505 ft. due to sediment aggradation within Prado Basin behind the dam (based on 2008 topography data). While most of the aggradation is due to the dam and flood risk management operations, some additional sediment deposition occurs when water is stored within Prado Basin for water conservation purposes. Scheevel Engineering (2015) estimated that an additional 3,500 yd3 of sediment deposition accumulates in the Prado Basin on an average annual basis when the buffer pool reaches 505 ft. This estimate assumed that the buffer pool would reach 505 ft. once per year, consistent with the proposed Water Conservation Plan.

The proposed sediment removal action would involve five primary activities; the construction of a sediment removal trap, construction of a sediment storage/green waste processing area, sediment removal by dry excavation, onsite storage/processing of the sediment material, and the hauling of the removed sediment. The sediment would initially be moved to the noted sediment storage site. Some of this sediment may be utilized for fill by the proposed project or other projects in the basin (i.e. Alcoa Dike), and any remaining fill would be hauled off site afterwards. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 10

The proposed sediment removal footprint would overlap with what is being implemented through OCWD’s sediment Demonstration Project (BO FWS-WRIV-09B0192-18F0101), which was initiated in the fall of 2019. Implementation of the herein proposed sediment removal measure would remain consistent with the conservation measures and requirements in the noted BO.

The noted sediment removal trap has already been constructed within the Santa Ana River in the southeast portion of Prado Basin near elevation 505 ft. The sediment removal trap currently and as proposed herein covers approximately 14.3 acres and would have a maximum excavation depth of 12 ft. when completed. Also, a 30-ft.-wide project access road has been constructed around the perimeter of the sediment removal trap and from the sediment removal trap to a sediment storage site.

In order to construct the sediment removal trap and project access road, all vegetation, including approximately 1.6 acres of native riparian vegetation, within the footprint of these facilities has already been removed. The vegetation removal occurred outside of bird nesting seasons per the Terms and Conditions of the Demonstration Project BO. As proposed, the sediment removal trap would be revegetated with native vegetation between sediment removal activities (roughly Project Years 1 and 25). At least a partial access road or path would remain unvegetated for continued access during the Project life. Vegetation would need to be cleared in the same sediment trap footprint prior to the second sediment removal event at approximately Year 25, following which both the sediment trap and access road would be restored with native vegetation.

An approximately 20.6-acre sediment storage site would be prepared by clearing or mowing surface vegetation in order to store the material excavated or dredged from the sediment removal trap. The area would be graded/re-contoured as necessary. Storage site preparation would take place outside of the California gnatcatcher nesting season. Consistent with the BO for the 5-year Planned Deviation, OCWD and/or the Corps would regrade and hydroseed the sediment storage location following completion of its use by this and a separate unrelated project (i.e., the Alcoa Dike project).

As proposed, a combination of dry excavation and hydraulic dredging would be used to remove sediment from the sediment removal channel area. The sediment removal method would be determined based on conditions at the time of sediment removal, and chosen to minimize any potential environmental impacts. Once the vegetation is removed, heavy equipment would begin excavation of the sediment removal channel to create a pool for hydraulic dredging. Once the pool is created, a hydraulic dredge would travel up and down the sediment removal channel. As the hydraulic dredge barge travels along the sediment removal channel, a discharge pipeline would trail behind floating on top of the water surface. In the event there is not enough water for the dredge to operate, the sediment would be removed by dry excavation. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 11

If a dredge is used, the collected slurry would be conveyed to the sediment storage site though a temporary 12- to 18-inch above ground discharge pipeline with the assistance of booster pumps. Once the sediment reaches the sediment storage site the slurry mixture would be deposited in settling basins for water removal. Once the water has been removed, the sediment would be stockpiled onsite. The dredged or excavated sediment would eventually be hauled offsite (a portion of this sediment may be used at the proposed Mill Creek Native Planting Site noted below).

Initial construction of the sediment removal features and the initial removal of 125,000 yd3 would occur within the first 5 years of the Project. At approximately Project Year 25, the final 125,000 yd3 would be removed from the trap area. Years in which sediment removal does not occur would include proposed annual wildlife and habitat monitoring as well as maintenance road upkeep.

Auto Center Drive would be used to access the measure site. Once on-site, existing maintenance roads would be used for access to the sediment trap. All associated worker parking, construction, sediment removal, and ongoing maintenance activities would be staged from within the footprint of the sediment storage site or from the Corps Prado Field Office.

Invasive Plant Management (All Focal Areas)

The purpose of this measure is to remove invasive plants from all focal areas (SARM Upstream, SARM Downstream, Chino Creek, and Mill Creek) to encourage the growth of new areas of native vegetation communities and to increase the biological values of existing native vegetation communities. After removal activity is completed, five years of herbicide treatment would occur to limit the reestablishment of non-native plant communities. Small stands of invasive plants intermingled with native plant species would be removed by hand operations with small equipment and hand tools. Large expansive stands of invasive plants would be removed with heavy equipment and large labor forces. Invasive plants would be chipped and processed as needed for re-use onsite or removal and disposal away from the focal area. Invasive plants that can be effectively processed to avoid regrowth could be re-used onsite as mulch. Excess biomass or invasive plant types that present a high probability of re-establishment would be disposed of offsite. As each area is cleared it would be evaluated by biologists to determine how to best manage that area. Supplemental plantings, pole cuttings, seeding, and maintenance of treated areas would be performed as necessary. Approximately 248 acres of invasive plants would be removed from the SARM Upstream Focal Area, 14 acres from the SARM Downstream Focal Area, 69 acres from the Chino Creek Focal Area, and 59 acres from the Mill Creek Focal Area (Figure 2). The acreages and precise locations shown in Figure 2 will be further refined during the Pre-Construction Engineering and Design (PED) phase, which would follow congressional authorization and funding.

As the measure would be implemented, monitoring for adaptive management would be conducted until the success criteria are met for the measure (see description of monitoring activities provided under Monitoring Objective 2, below). After the success criteria listed under Monitoring Objective 2 have been met, adaptive management actions would cease, and routine Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 12

maintenance would be conducted. Maintenance would include routine inspections to detect re- infestation by invasive plants and spot treatments to prevent re-establishment of invasive plants in treated areas.

Existing maintenance roads and trails would be used for access to invasive plant removal areas. Within all focal areas, some invasive plant zones would be accessed across previously cleared areas prior to native plant regrowth or new plantings. All worker parking, biomass processing and ongoing maintenance activities would be staged from within the footprints of the removal areas, at the Chino Creek Native Planting Area, or at the OCWD Prado Field office.

Proposed Invasive Plant Management activities would begin in Project Year 1. After each year of biomass removal, 5 years of herbicide treatment would occur. Following this, until Year 50, OCWD would perform regular inspections and maintenance as part of the Project, including targeted herbicide treatments with the goal of ensuring that invasive plant communities do not reestablish in the area where non-natives were removed during the 50 year Project life. The Service would be provided with maps, including acreages, showing where the invasive plant stands have been identified for removal prior to beginning work, and OCWD would continue to provide updates on maintenance work until Year 50.5

Chino Creek Channel Restoration

The intent of this measure is to partially re-route the existing flows in Chino Creek through a new channel and floodplain area to be constructed along the west side of the current creek alignment, with the goal that this new creek section would support increased area of native riparian vegetation communities compared to existing conditions. Currently, the Corps has about 30 percent of the design of this measure developed; the Corps has indicated they are committed to working with the Service as they refine the details of this measure’s construction and implementation.

As proposed, the inflow at the north (upstream) end of the measure area would be split to provide flows to the new channel and to maintain some reduced portion of the current flow in the existing Chino Creek alignment, with the goal of some continuing support of the aquatic and riparian natural communities in the existing creek section.

The new channel would have a higher invert than the parallel existing creek channel section. Proposed construction activities would include grading to create a new channel and associated perimeter berms. The new creek channel is not anticipated to be more than 3 ft. deep. The low- flow containment berms would be used to guide overbank water flows and help ensure that flows from the new channel do not immediately return to the existing channel. These berms are expected to support riparian scrub and transition to a riparian forest plant community closer to the new creekbed section. A portion of the existing Chino Creek channel invert at the northern end of the main footprint area for the measure would be filled in order to force some creek flow into the new channel. A valve and pipe would be installed (and maintained for the life of the

5 As proposed, no specific recurrent reporting (such as annual reports indicating locations and measure effectiveness) is required to be sent to the Service as part of this measure. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 13

Project) at the upstream extent of the new channel to control and split creek flow into the remaining existing creek section. To reduce channel erosion and to help control the hydraulic grade of the new channel, a grouted stone invert stabilizer would be constructed immediately downstream of Pine Avenue, and a partially concrete-grouted and ungrouted stone drop structure would be constructed in Chino Creek. A pool and riffle structure would be constructed at the outlet of the proposed diversion pipe, and a bio-engineered invert stabilizer would be installed at the downstream end of the newly constructed channel. The pool and riffle structure and the bio- engineered invert stabilize structures would be designed based on a roughened channel concept, with ungrouted gravel, cobbles, and boulders, to allow for fish passage. They would also have willow cuttings included in the structures to provide habitats and food sources for birds, and cover for aquatic species.

The initial activities would include clearing and grubbing the footprints of the new channel alignment, berms, maintenance road, drop structure, outlet, invert stabilizer, and Chino Creek fill area. Vegetation removed would be mulched and used in the project area or elsewhere within Prado Basin. Excess biomass or invasive plants that present a high probability of re- seeding/regrowth would be disposed of offsite. All vegetation processing activities would take place within the footprints of the new channel area or the creek fill area. The clearing and grubbing phase of the project would start in the fall to avoid bird nesting seasons and to avoid storm flows in Chino Creek.

Fill material would be utilized to grade and construct the perimeter berms along the new creek alignment, fill a portion of the existing creek section, and install the invert stabilizers and new diversion pipe. The total volume of earthwork would be approximately 175,000 yd3. The soil excavated from the new channel alignment would be used to fill a portion of the existing creek channel, construct the surrounding berms, and grade/level the adjacent areas around the new creek channel. The perimeter berms along the new creek alignment would be approximately 3 ft. high (with a 12 ft. wide flat top to the berms for a maintenance road/potential passive recreation trail) and 28 ft. wide at the base with 3:1 side slopes. Any excess earthwork cut would be spread in adjacent overbank areas out of the targeted habitat restoration area.

The section of Chino Creek that would be filled includes two sections. The upstream-most section of the creek would receive partial fill to increase the Chino Creek invert. This section would continue to receive some creek flows. Downstream of this partial fill, a section of the creek near the new diversion pipe would be completely filled and no longer receive water. This section is approximately 500 ft. long by 35 ft. wide. This would result in a direct loss of open water surface area of approximate 0.40 acres. The approximate area of new open water surface created by the spreading of water in the new channel would 4,700 ft. long by 30 ft. wide (3.24 acres), potentially resulting in a net gain of approximately 2.84 acres of open water surface area. Native plantings would be a part of the final phase of the measure to help accelerate the development of native natural community types.

Wildlife fencing along both sides of portions of Pine and Euclid Avenues would also be installed as part of this measure. A total of approximately 3.2 miles of fence would be constructed along these roadways to help direct wildlife to undercrossing entrances. The fence alignments would Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 14 initially be cleared of vegetation to a 30-ft width to facilitate construction. However, once construction is complete, approximately ½ of the fence buffer zone footprints (15 ft. wide) would be kept free of vegetation to provide access to the fences and culverts for maintenance.

As shown in Table 2, implementation of the Chino Creek Channel Restoration Measure would require the direct removal of 5.27 acres of willow/cottonwood vegetation communities and 0.07 acres of mixed riparian vegetation communities. Trails through the channel area would be used to provide access to remove sediment and debris, and to facilitate habitat maintenance, including non-native vegetation management.

Table 2. Summary of Direct Impacts to Vegetation/Natural Communities of Proposed Chino Creek Channel Restoration Measure

Acres Vegetation/Natural Communities Directly Affected Affected Aquatic 1.66 Willow/Cottonwood 5.27 Mixed riparian 0.07 Coastal sage scrub 0.0 Coastal sage scrub/Non-native weeds 0.0 Non-native weeds 111.49 Eucalyptus 0.37 Arundo 0.0 Disturbed 0.0 Urban 1.47 Total 120.29

Construction activities would start in Year 3 in the Chino Creek Focal Area. Construction of the measure features would take approximately 4 months.

All worker parking and construction activities would be staged from within the footprint of the raised invert and new channel cut areas. Long-term maintenance activities would be staged from the maintenance road within the project measure’s footprint.

Once the reconfiguration of Chino Creek channel is completed, the Chino Creek Chanel Restoration Measure footprint would be planted with native riparian vegetation. The riparian species planted would primarily consist of willow and mulefat, however, the plant species list for all native plantings and other details will be refined during the Corps PED phase. During the maintenance period, OCWD would incrementally install and maintain new native plantings on an as-needed basis for 10 years.

Non-native vegetation communities would be removed during construction, followed by 5 years of herbicide treatment. After the initial removal of non-natives in the Chino Creek Restoration Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 15

area, OCWD would actively maintain these areas to allow for natural recruitment of natives as ongoing follow-up non-native removal occurs.

Following construction, monitoring will be conducted and adaptive management implemented as necessary until the success criteria, as detailed in the description of monitoring activities provided under Monitoring Objectives 1 and 2, below, are met.

Maintenance of the measure would begin in Year 4 after construction is complete and occur annually from Year 5 through Year 50. Maintenance activities would occur annually during low flow periods in the creek and outside of bird nesting seasons. Biologists would inspect the work areas prior to maintenance activities to help avoid impacts to wildlife. The schedule of the maintenance activities would be would vary from year to year as conditions change. Biomass and debris generated from storm flows would be removed from the channel annually. The maintenance road and seasonal/temporary trails through the channel area would be used to provide access to remove sediment and debris and to facilitate habitat maintenance, including non-native vegetation management. Annual trimming and mowing of vegetation would provide access to areas in need of maintenance. The maintenance activities would be performed under the direction and supervision of biologists to help ensure that maintenance activities do not diminish the habitat functions of the associated channel and creek areas. Maintenance activities would include trimming and maintaining vegetation around the channel, maintenance road, berms and in-channel structures. Invasive plants would also be removed from the area on an annual basis. The work would be done under the direction and supervision of a biologist to help ensure no wildlife are disturbed. Native vegetation would be managed, and if necessary re- planted, in areas significantly damaged by storm flows or in areas where significant disturbance to native plants occurs. An Operations, Maintenance, Repair, Replacement, and Rehabilitation (OMRR&R) Manual for this feature would be developed by Corps engineering staff following construction. The OMRR&R Manual would be based on the final design and as-built condition, and would describe the required operations and maintenance for this feature.

Native Plantings (Chino Creek)

The Native Planting Measure includes activities within the Chino Creek Focal Area to develop an enhanced habitat area in an open field east of Euclid Avenue and immediately north of Pomona Rincon Road. The 42.9-acre site would be cleared, grubbed and re-graded to achieve proper drainage. The site would be replanted with native riparian species; plantings would include seeding, pole staking, and planting of container plants at select locations across the site. Approximately 42 acres of the site is planned to be converted to riparian forest and scrub habitats. Approximately 30 acres closest to Chino Creek would be converted from existing ruderal and non-native grassland plant communities to riparian forest habitat. Forested habitats would be dominated by willow species, including black willow (Salix gooddingii) nearest the water’s edge, with other willow species including, but not limited to, arroyo willow (S. lasiolepis) and red willow (S. laevigata) slightly further from the creek bank. The remaining 12 acres of the site would be converted to riparian scrub dominated by mulefat, with various willow and other riparian associated species also present. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 16

A new maintenance road would be constructed to provide maintenance for the bioengineered grade control structures. A staging/parking area would be also be constructed to provide a workspace for monitoring and habitat maintenance. The proposed all-weather maintenance road driving surface would be approximately 10 ft. wide with an additional 2.5 foot wide shoulder along each edge. The road shoulders would be kept clear and maintained to allow for drainage and allow for maintenance equipment to pass. The staging/parking area would measure 40 ft. x 200 ft. The total decomposed granite surface area of the road and staging area would be approximately 0.55 acres. The parking area and maintenance road are not expected to be able to be used by the public (e.g., for recreation).

The initial construction and planting activities associated with the Native Planting Measure at Chino Creek would be implemented in two phases over a period of approximately 3 months during the fall of Year 2 of the Project’s implementation. Phase 1 would involve invasive plant removal, clearing/grubbing, and grading activities to establish appropriate hydrology and construct the maintenance road and staging area. Grading activities would use a balanced cut and fill method to use the existing soils on-site. Areas of existing native vegetation that are near the finished design grade would be protected in-place and not be disturbed. Up to 42.9 acres would be affected by the measure, consisting of 0.4 acres of black willow riparian natural community, and the remainder consisting of mowed ruderal field. The total maintenance road corridor would measure approximately 15 ft. wide, extending from Pomona Rincon Road to the east and south approximately 1,600 ft. Of the 42.9-acre direct footprint, the total area of permanent impact from the parking area and the maintenance road would equal approximately 0.73 acres. The remaining 42.17 acres would consist of temporary impacts.

Native and invasive plants cleared from the restoration area would be processed and chipped as needed for use onsite or removal and disposal from the focal area. Invasive plants that can be effectively processed to avoid regrowth may be used onsite. Excess biomass or invasive plants that present a high probability of reestablishment would be disposed of offsite. All construction staging and vegetation processing activities would take place within the footprint of the native planting area. The clearing and grubbing phase of the project would start in the fall to avoid bird nesting season. Wildlife monitoring would occur during clearing and grubbing with the goal of avoiding impacts to late nesting birds and other wildlife.

Phase 2 activities include those required to finish grading the native planting area, road, and staging area, and to restore portions of the site disturbed by the construction activities. Site restoration would involve planting of native vegetation communities over the 42.17-acre site. During restoration work and maintenance, all worker parking, construction deliveries, and maintenance activities would be staged from within the footprint of the native planting area, the maintenance road and/or the staging area.

Monitoring and adaptive management of the measure would begin immediately following the completion of planting and continue for 5 years. As the measure is implemented, monitoring for adaptive management would be conducted until the success criteria are met for the measure. See description of monitoring activities provided under Monitoring Objective 2, below. After the Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 17 success criteria listed under Monitoring Objective 2 have been met, adaptive management actions would cease, and maintenance would be conducted for 10 years.

Maintenance activities would occur annually during low flow periods in the creek and outside of the bird nesting seasons. Biologists would inspect the work areas prior to maintenance activities with the goal of avoiding impacts to wildlife. The schedule of the maintenance activities would vary from year to year as conditions change.

Maintenance activities may be performed in two separate phases. Phase 1 maintenance activities would include those required to trim and maintain vegetation along the maintenance road, staging/parking area, and within the 42.17-acre native planting area. Any new growth of invasive plants would also be removed from the site. Maintenance work would be done under the direction and supervision of a biologist. Hand labor may be used at times to avoid damage to high function habitats.

Phase 2 maintenance activities include grading to reshape or restore the maintenance road and staging/parking area. Debris from storm events would be removed from the road and minor grading would occur to reshape the road where damage had occurred from storm flows or normal wear-and-tear. Decomposed granite would be imported annually to re-dress the top of the road and staging/parking area. This phase of maintenance would start in the early spring (typically late February) once storm flows have receded, prior to springtime nesting activity. Wildlife monitoring would occur during road maintenance to avoid impacts to wildlife.

Native Plantings (Santa Ana River Mainstem Upstream)

The Native Planting Measure includes activities within the Upstream SARM Focal Area to develop an enhanced habitat area in an open field between the Santa Ana River and the existing OCWD Wetlands Diversion Channel (this area is adjacent to but does not overlap with 228 acres of existing mitigation in-place for previous water conservation activities). The approximately 45- acre site would be cleared, grubbed and re-graded to achieve desired drainage. Some grading would be required to remove sediment or fill on the site in order to get the ground surface level closer to the groundwater table to aid in the success of plantings. The site would be replanted by seeding, pole staking, and planting of container plants at select locations. Areas of existing native vegetation that are near the design finished grade would be protected in-place and not disturbed. Approximately 35 acres of the site that is currently dominated by non-native grasses would be converted to riparian forest natural community dominated by willow (Salix spp.).

The initial construction and planting activities associated with the Native Planting Measure at Upstream SARM would be implemented over a period of approximately three months in the fall of Year 1 of the Project’s implementation. Native and invasive plants cleared from the measure area would be processed and chipped onsite for removal and disposal from the focal area. Invasive plants that can be effectively processed to avoid regrowth may be reused onsite. Excess biomass or invasive plants that present a high probability of re-seeding/regrowth would be disposed of offsite. All construction staging and vegetation processing activities would take place within the footprint of the native planting area. This phase of the project would start in the Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 18 fall. Wildlife monitoring would occur during clearing and grubbing with the goal of avoiding impacts to late nesting birds and other wildlife. Grading activities would use a balanced cut and fill method. The final construction activities would be to restore portions of the site disturbed by the construction activities.

Monitoring and adaptive management would begin in Year 2 and continue until success criteria have been met. This is estimated to be a 5-year period. See description of monitoring activities provided under Monitoring Objective 2, below. After the success criteria listed under Monitoring Objective 2 have been met, adaptive management actions would cease, and routine maintenance would be conducted for 10 years.

Maintenance activities would occur annually during low flow periods in the Santa Ana River and outside of the bird nesting seasons. Biologists would inspect the work areas prior to maintenance activities to avoid impacts to wildlife. The schedule of the maintenance activities would vary from year to year as conditions change. Maintenance activities would include those required to encourage the development of native vegetation. New growth of invasive plants would also be removed from the site annually. Maintenance work would be done under the direction and supervision of a biologist. All worker parking, construction deliveries and long-term maintenance activities would be staged from within the footprint of the native planting area and from the OCWD Prado Field Office.

Native Plantings (Mill Creek)

The Native Planting Measure includes activities within the Mill Creek Focal Area to develop an enhanced habitat area in an existing shallow basin (Pond E-3 of the existing OCWD water treatment pond) located southwest of the OCWD Prado Field Office. The 17.21-acre site would be cleared, grubbed, and partially filled with material from the sediment trap to achieve the desired elevations so that proper drainage could occur to support the design general natural community type. Perimeter drainage would be maintained by grading a shallow channel around the southern edge of the site. No major hydrological modifications are proposed at the Mill Creek native planting area, although grading would be required to prepare the site. Areas of existing native vegetation that are near the design finished grade would be protected in-place, but the majority of the site would be temporarily disturbed.

Details of grading requirements would be developed during the Corps’ PED phase when detailed designs are prepared. The site would be replanted by seeding, pole staking, and planting of container plants across the site. Per the proposed measure, approximately 16 acres of freshwater marsh would be converted to riparian forest dominated by willow species, including black willow, arroyo willow, and red willow.

The initial construction and planting activities associated with the Mill Creek Native Planting Measure would be implemented over a period of approximately three months during the fall of Year 2 of Project’s implementation. Native and invasive plants cleared from the measure area would be processed and chipped as needed for re-use onsite or removal and disposal from the focal area. Invasive plants that can be effectively processed to avoid regrowth may be reused Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 19

onsite. Excess biomass or invasive plants that present a high probability of reestablishment would be disposed of offsite. All construction staging and vegetation processing activities would take place within the footprint of the native planting area. This phase of the project would start in the fall as to avoid the bird nesting seasons. Wildlife monitoring would occur during clearing and grubbing to avoid impacts to late nesting birds and other wildlife.

Monitoring and adaptive management would begin following the completion of the plantings and continue for 5 years. See description of monitoring activities provided under Monitoring Objective 2, below. After the success criteria listed under Monitoring Objective 2 have been met, adaptive management actions would cease, and maintenance would be conducted for 10 years.

Maintenance activities would occur annually during periods outside of bird nesting seasons. Biologists would inspect the work area prior to maintenance activities to avoid impacts to wildlife. The schedule of the maintenance activities would vary from year to year as conditions change. Maintenance activities include those required to encourage the development of native vegetation. New growth of invasive plants would also be removed from the site annually. Maintenance work would be done under the direction and supervision of a biologist. Hand labor may be used to avoid negative impacts and avoid damage to higher function habitats. All worker parking and construction activities would be staged from within the footprint of the native planting area and from the OCWD Prado Field Office. Maintenance activities would be staged from the OCWD Prado Field Office.

Cowbird Trapping (Santa Ana River Mainstem Upstream, Mill Creek, Chino Creek)

The proposed Cowbird Trapping Measure would expand upon existing brown-headed cowbird6 trapping efforts ongoing in the Project area, by increasing cowbird trap numbers within and surrounding Prado Basin. The measure would include the trapping and removal of some cowbirds within the SARM Upstream Focal Area, the Chino Creek Focal Area, and the Mill Creek Focal Area. The proposed cowbird trapping would not overlap or replace ongoing trapping efforts in the area, but rather expand the control of cowbirds within the proposed Project focal areas. Cowbird trapping efforts would be integrated and coordinated with other ongoing efforts to ensure additive benefits and to cover additional areas not currently trapped. The current Corps cowbird trapping efforts in the region are predicted to decline in the future, as the construction- related commitments (including cowbird trapping) for various components of the Corps’ Santa Ana River Project are completed, necessitating a new program for cowbird trapping in the region (Corps 2019a).

The proposed cowbird trapping measure would provide for up to 7 traps within each of the SARM Upstream, Chino Creek, and Mill Creek focal areas; the exact location and number of traps have not been defined and are expected to change over time as needed to control cowbirds in these areas. As proposed, cowbird traps would be checked and maintained regularly. Proposed

6 The brown headed cowbird (Molothrus ater) is an avian species that was formerly restricted to grassland habitats in North America and has now spread across the continent facilitated by anthropogenic changes in land use including agriculture (Lowther 2020). It parasitizes the nests of many songbirds of the region, including threatened and endangered species. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 20

regular monitoring across the focal areas of the Project would identify which locations would benefit the most from cowbird trapping. Proposed cowbird trapping would start in September of 2021 (Year 1) in the upstream section of the focal areas. Cowbird trapping would be implemented for 5 years. Following the initial 5 years of the proposed cowbird trapping, regular inspection of the focal areas would be performed for the 50-year life of the project. The Project goal is to maintain less than 10 percent nest parasitism annually in each of the noted focal areas.

Monitoring and Adaptive Management

The monitoring below is associated with the Project’s proposed ecosystem restoration components only. The Corps anticipates that five years of monitoring and adaptive management would likely be sufficient for successful establishment of native riparian vegetative cover and abatement and control of non-native wildlife, per the proposed Project.7 However, once the Corps determines that ecological success for a measure has been fully achieved, even if this occurs in less than 5 years, no further monitoring would be performed. If performance criteria for project objectives have not been met within the first 5 years, then cost-shared monitoring with OCWD and adaptive management would continue within those areas until performance criteria are met, or for a maximum of 5 additional years, whichever is less, resulting in no more than 10 years of cost-shared monitoring. For the proposed Project measures that involve restoration of in-stream hydrologic, geomorphic, and topographic conditions, such as with the Chino Creek restoration, 10 years of monitoring and adaptive management may be needed, as these measures are expected to require more time to achieve success criteria due to the episodic nature of flood cycles in relation to the restoration process. If the success criteria cannot be met within the 10- year period of cost-shared monitoring, any additional monitoring and management would be OCWD’s responsibility.

The Corps and OCWD would document the monitoring results, assessments, and the management outcomes, producing annual reports that would measure progress towards meeting the Project’s objectives, as characterized by the Project’s performance measures. Results of assessments would be used by the Corps and OCWD to evaluate adaptive management needs and inform decision-making.

Monitoring Objective 1: Improve hydraulic and fluvial geomorphic functions to promote habitat growth and wildlife connectivity to regionally significant core habitats at Prado Basin and associated main watercourses within the proposed project area. The goal is to increase the structure and diversity of in-channel form and microhabitats in the Chino Creek focal area.

To assess the overall stream health and available habitats for native fish and wildlife movement, a California Stream Bioassessment Worksheet would be completed annually for 5 years at three permanent monitoring stations within the restored channel area of Chino Creek. Geomorphology

7 According to correspondence with the Corps, the purpose of the Monitoring and Adaptive Management measure proposed herein is “to establish that the project was initially successful at meeting project objectives and providing the estimated benefits, so that is what this statement is in reference too. We believe that the 5 year period will be sufficient to initially meet the project’s objectives and projected benefits, while future maintenance will ensure that these benefits are maintained.” Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 21

and in-channel habitat elements will be monitored, including stream gradient, channel form, dimensions, substrate composition and distribution. Vegetative cover above the stream will also be assessed. Cross-section locations would be determined in the Pre-Construction Engineering and Design phase.

Methods involve placing a transect line perpendicular to flow at the up and downstream extents of 328-ft (100-meter) monitoring sites. Substrate composition and size (silt, sand, gravel, cobble, boulder, sandbars, and emergent vegetation), channel width, channel depth, mid-column current velocity, and riffle/pool microhabitat depths and velocities will be measured at 3.3 ft. (1.0 meter) intervals along each transect line.

Monitoring of these geomorphic features is necessary to determine the successful establishment of a stable, native arid southwestern stream channel. Changes to geomorphic processes will affect the vegetation component of target habitats, which would also impact wildlife movement through the project area. If vegetative cover and structure criteria are not being met, data from monitoring of geomorphic and hydrologic processes may provide additional information on the underlying causes of failure.

Success Criteria: Geomorphic and in-channel habitat elements should achieve diversity within 3 years post-construction, as compared to reference sites; monitoring results should show sinuosity, riffle-pool-run complexes, and multiple depths within the channel. Desirable geomorphic conditions would be evaluated using reference sites on the Santa Ana River or other sites of similar hydrologic character and gradient to guide quantitative thresholds for channel form and substrates.

Monitoring Objective 2: Restore riparian and riparian-associated habitats suitable to native species within the proposed project area. The goals are to: increase percent cover of native riparian and riparian-associated habitats, maintain appropriate structural diversity of native riparian habitats to support survival and reproductive requirements for riparian obligate species and to support regional wildlife movement, increase percent native vegetative cover over water to reduce water temperatures to support native fish such as the Santa Ana sucker and arroyo chub, and decrease percent cover of non-native invasive vegetative species that out-compete natives.

The Corps would establish permanent quantitative vegetation transect monitoring stations for assessing vegetation communities at each of the native planting locations, as well as within each of the invasive plant management areas. The final number of transects at each location will be determined based on the size of the feature and the type of habitat being restored, with consideration given to the number of transects required to capture natural variability within the reference sites for each habitat type. The Corps estimates that Chino Creek and Mill Creek would require 5 transects, while features in the SARM upstream and downstream focal areas would require 10 transects. Sampling will occur during spring months, at the peak of growing season, and will consist of permanent field monitoring plots along one or more transects either perpendicular to the stream centerline or parallel to the floodplain slope and hydraulic gradient. Plots would be located randomly within each focal area, and the distance between plots and Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 22 along transects will be dependent on the conditions and variability in the focal area. Monitoring will measure percent cover of native and non-native plant species, structural diversity, and percent cover over water. Photograph stations are also important for documenting vegetation conditions. All plots and photograph stations will be documented via Global Positioning System (GPS) coordinates to reoccupy in each year of sampling.

General observations, such as fitness and health of plantings, native plant species recruitment, plant composition and structure, and signs of drought stress would be noted during the surveys. Additionally, potential soil erosion, flood damage, vandalism and intrusion, trampling, and pest problems would be qualitatively identified. Analysis of hyperspectral imagery mapping from OCWD would be performed during 2 of 5 monitoring years. This analysis would ensure comprehensive assessment of non-native cover in the project area and identify problem areas that may require adaptive management.

These stations would be monitored annually for 5 years post construction and would continue to be monitored long-term as part of operation and maintenance. In addition, during the initial year of monitoring, data from reference sites will be collected for comparison. Reference sites will be chosen from within the Prado Basin by the Adaptive Management Team (AMT).8 A reference site for each natural community type restored will be identified (i.e. riparian woodland, riparian scrub, and transitional riparian). Monitoring will measure percent cover of native and non-native plant species, structural diversity, and percent cover over water. This monitoring will indicate if target habitats have been successfully restored, habitat connectivity established, and increased wildlife movement supported.

Inventories of general wildlife would be documented annually post construction for 5 years, in addition to a baseline inventory taken during the first annual vegetation monitoring effort. In addition to general wildlife surveys, focused wildlife surveys, including protocol surveys for vireo and flycatcher will be performed annually for 5 years post-construction, in addition to a baseline survey. Focused amphibian and reptile surveys would be performed at baseline, as well as Year 1, Year 3, and Year 5 after construction. Native fish surveys would be performed annually for 5 years, plus baseline.

Bird counts from permanent monitoring stations would be taken twice annually for 5 years, as well as during the baseline to document the differences between wintering and nesting season bird species diversity and locations. Data on large mammal use would be compiled at baseline and quarterly thereafter from studies performed by existing USGS monitoring programs and from camera traps in the Prado Basin. Roadkill counts would also be used to document wildlife movement patterns.

Monitoring of vegetation (including percent cover, structural diversity, cover over water, and cover of invasives) will indicate if target habitats and the hydrology that supports them have

8 The Adaptive Management Team will be composed of the Corps, OCWD, and potentially the US Fish and Wildlife Service, the California Department of Fish and Wildlife, and the Santa Ana Regional Water Quality Control Board. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 23

been successfully restored.9 Results of monitoring for vegetation communities would also indicate whether habitat components necessary to provide habitat connectivity and support increased wildlife movement have been successfully established. Wildlife monitoring should show a trend of maintaining or increasing use or movement by common native riparian obligate species and/or target or special status species, as compared to previous studies conducted by USGS and existing regional wildlife movement and use patterns.

Success Criteria: Restoration of riparian habitat would be reached when 50 percent cover of native riparian habitats (including herbaceous, shrub and canopy layer) is achieved within 250 ft. of the river channel (based on locations of restoration of each habitat) within 3 years, and 75 percent cover of native riparian habitat is achieved within 5 years. Farther than 250 ft. from the river channel, restoration of riparian habitat would be reached when 35 percent cover of native riparian habitats (including herbaceous, shrub and canopy layer) is achieved (again, based on locations of restoration of each habitat) within 3 years, and 50 percent cover of native riparian habitat is achieved within 5 years. Canopy cover should not exceed 60 percent and/or shrub cover should exceed 50 percent within 5 years. The Corps also proposes that percent cover of riparian vegetation over water along the bank should achieve 25 percent within 3 years and 40 percent within 5 years in order to reduce water temperatures to support native fish. Non- native, invasive vegetative species percent cover should be reduced to less than 10 percent after 3 years and less than 5 percent after 5 years.

Monitoring Objective 3: Reduce presence and effects of non-native wildlife on habitat suitability and function for native wildlife species. The goal is to reduce the brown-headed cowbird population and associated nest parasitism to support use and occupation of riparian habitats by endangered vireos and flycatchers.

Cowbirds would be monitored and counted annually for 5 years through the general wildlife inventories. Parasitism of vireo nests by cowbirds would also be monitored at baseline and Year 1, Year 3, and Year 5. Monitoring for cowbirds will indicate if target habitats are less suitable due to the potential for nest parasitism, which may inhibit occupation by and populations of riparian obligate songbirds. Results of this monitoring will inform whether adaptive management actions related to cowbird control are needed, and which focal areas would benefit most from removal.

Success Criteria: Cowbird trapping will be considered successful when less than 10 percent of nest parasitism is maintained annually within the Study area and wildlife monitoring shows trends of decreasing cowbird populations with either no change or an increase in population of riparian obligate songbirds, including vireos.

9 According to correspondence with the Corps, groundwater monitoring will not be included in the revised MAMP. All features in the MAMP are cost-shared portions of the project until success is achieved, or until the 10-year limit has been reached. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 24

Conservation Measures

To avoid, minimize, and offset impacts to federally listed species and their designated critical habitats, general and species-specific conservation measures listed below would be implemented in portions of the Project area where sensitive resources may occur.

General Conservation Measures

CM1: All vegetation clearing and sediment removal activities and the operation of heavy construction equipment will be conducted between September 16 and February 28, outside of bird nesting and fish spawning season. Vegetation removal and the operation of heavy equipment may begin in the month of August provided the area is surveyed by a Service-approved qualified biologist in advance of vegetation removals and the qualified biologist determines that no nesting birds are present within 500 feet of the activities.

CM2: To avoid impacts to sensitive wildlife species, a qualified biologist approved by the Service will conduct a biological resource sweep of the work area prior to any ground disturbing activities, during project operation and during demobilization of construction equipment. The biological resource sweep will include the following activities:

• Inspect the work area for any wildlife species, prepare a list of species observed, and record their activity during construction and operation of the project. • Ensure that habitats within the construction activity impact area are not occupied by sensitive wildlife species. • Monitor access roads to ensure sensitive wildlife is not impacted by construction equipment. • In the event sensitive wildlife species are present, determine if the activity would cause adverse impacts. If it is determined that the activity could have the potential to adversely affect listed species, the activity will cease until the species is no longer in harm’s way.

CM3: During vegetation removal activities, vegetation planned for removal will be inspected to determine if nests are present. If nests are present, the biologist will evaluate the nest site for activity and, if possible, determine species, and will propose avoidance measures and/or buffers, as appropriate.

CM4: Ecosystem restoration activities conducted within Santa Ana River, Chino Creek and Mill Creek would occur between August 1 and January 15, outside of the sucker spawning season.

• In addition, prior to the start of grading activities for the Chino Creek Channel Restoration Measure, a native fish survey will be conducted in Chino Creek. If native fish (sucker; Arroyo chub [Gila orcuttii]) are detected, the Corps coordinate further with the Service on the implementation of this measure.

Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 25

CM5: Vehicles and other equipment will be fueled, cleaned and maintained in designated areas, located away from the Santa Ana River, Chino Creek and Mill Creek to eliminate risk of pollution from spills and contamination.

CM6: Construction personnel will use designated access roads or previously disturbed areas for vehicle access and staging of construction equipment.

CM7: Unpaved areas will be watered as needed to control dust on a continual basis during construction.

CM8: All construction, site disturbance and vegetation removal will be located within the delineated construction boundaries. The storage of equipment and materials and temporary stockpiling of soil would be located within designated areas outside of habitat areas.

CM9: Prior to removal of vegetation, access routes in and out of the project area will be flagged. Areas to remain undisturbed will be clearly flagged or otherwise delineated prior to construction activities and will be monitored to ensure that all activities do not encroach into the delineated protected areas. The qualified biologist will have the authority to halt the vegetation management activities if occurring inside delineated protected areas.

CM10: A litter control program will be implemented during construction to eliminate the accumulation of trash. Trash will be removed from trash receptacles at the end of each work day to discourage wildlife movement into work areas.

CM11: Speed limits of 15 miles per hour or less will be required at all times to avoid potential injury to wildlife in the area.

Water Conservation Plan Measures

CM12: OCWD has been monitoring habitat conditions within the Plan Area to measure effects associated with the previous 5-year Planned Deviation to the Water Control Plan. Those monitoring efforts will be continued in a Habitat Monitoring Plan prepared by OCWD in coordination with the Corps, US Geological Survey (USGS) and the Service and will include a statistically robust sampling method to measure and analyze effects of inundation on riparian vegetation. The vegetation will be monitored annually for signs of degradation. If the habitat monitoring program indicates substantial changes (>30 percent loss of foliage) and prolonged degradation of vegetation between 498 and 505 feet, the affected habitat will be given 2 years to recover on its own (the season of inundation and the following season), prior to active planting. The degraded habitat will be restored within the same area if possible, within two years after the 30 percent degradation trigger is detected. Restoration can either occur through natural recruitment, non-native removal, active planting or some combination.

Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 26

• If the degraded habitat does not recover within that 2-year timeframe, OCWD will plant and/or restore the same amount of vegetation (equal in size to the degraded area, 1:1 ratio) in place or on OCWD property above 505 feet in elevation, and they will continue to maintain this area for the life of the Plan. • Areas that were inundated above 505 feet for more than three (3) days will also be monitored, and if the vegetation is not found to have recovered after two years of monitoring, the Corps and/or OCWD will replace on Corps and/or OCWD property as above.

CM13: This measure replaces Conservation Measure 4 of Service 2002a (FWS-WRIV-2102.3). For the life of the project, OCWD will implement a predatory aquatic species control program from one of the measures listed below:

• In Sunnyslope Creek, a tributary of the Santa Ana River near Riverside, provided that flow can be maintained in Sunnyslope Creek at a suitable flow rate and Santa Ana Sucker are observed in the creek; a suitable flow rate is a rate that is enough to keep aquatic habitat viable year-round and to maintain hydrologic connectivity with the river during the spawning season. The effort will be equivalent to 15 person days (not less than 255 hours in the river) and efforts to control marsh vegetation, sedimentation, trash or gradient can be counted to the effort; • Fifteen person-days (not less than 255 hours in the river) per year of mechanical removal of predatory aquatic species at a location identified in coordination with the Service o In the event OCWD implements a sediment removal project in the vicinity of the Santa Ana River at the River Road Bridge Crossing, predatory aquatic species removal at this project location is presumptively considered to be an appropriate location to fulfill the requirements of CM13

Either measure listed above may be implemented at different time periods over the life of the project, but in each year one or the other will be implemented. OCWD will coordinate regularly with the Service regarding this effort and when agreeable to both the Service and OCWD, other measures to benefit the sucker may be undertaken instead of either of the measures listed above. Predatory aquatic species control measures will only occur outside the spawning season (i.e. they will occur between September 16 and January 15). OCWD will provide a report to the Service annually, describing the effort undertaken.

CM14: This measure refines previous OCWD commitments related to water conservation as described in the 2018 5-year deviation BO (FWS-WRIV-09B0192-18F0101), as well as the 2015/2016 and 2016/2017 single-year deviation BOs (FWS-WRIV/OR16B0174- 16F0322-R001 and FWS-WRIV/OR16B0174-16F0322-R002, respectively). The Corps and/or the OCWD will complete the following tasks to collect water quality data for water flowing into Prado Basin and water released from Prado Dam:

• Evaluate and compare water quality (dissolved oxygen, turbidity, temperature, nitrate, nitrite, ammonia, organic nitrogen, phosphate, total dissolved solids) between base Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 27

flows and storm flows (independently) entering Prado Basin (from Mill Creek, Chino Creek and Santa Ana River) and discharged from Prado Dam to identity changes in water quality associated with operating Prado Dam (e.g., holding water behind the dam): o Water quality for water entering Prado Basin will be assessed at three locations upstream of Prado Dam: Chino Creek at Pine Avenue crossing, Mill Creek at Chino Corona Road crossing, and the Santa Ana River at River Road crossing o Water quality for the water discharged from Prado Dam will be assessed at the Santa Ana River below (downstream of) Prado Dam location near the State Highway 71 crossing o Water quality above Prado Basin and below Prado Dam will be compared in order to determine if dam operations are contributing to changes in water quality o Water quality samples will be collected over a three-year time period at four baseflow water quality samples will be collected in July or August of each year, as well as monthly samples between November through April; over the three- year period, a total of three storm events will be targeted for stormwater sampling at the four sampling locations, if the three-year period does not have sufficient precipitation to cause stormwater runoff events, then one additional year will be added to the duration of sampling in an attempt to collect a total of three stormwater runoff events over the four-year time period. o Annual reports will be prepared and provided to the Service documenting the data collected in the previous year; after the last sampling event is concluded, a report will be provided containing all of the data.

CM15: OCWD will collect ground surface elevation data to define topographic cross sections at the following four locations on the Santa Ana River:

• Downstream of the drop structure near the La Cadena Avenue crossing in Colton • A location between the Rapid Infiltration Extraction (RIX) Facility in Colton and the Market Street crossing in Riverside • The Hamner Avenue crossing in Norco • The River Road crossing in Eastvale

The ground surface elevation data would be collected during a low flow condition in the summertime and is intended to capture the entire cross section of the Santa Ana River, including the low flow channel. Ground surface elevation data will be collected on the following schedule:

• Once per year for Years 1 through 10 • Once in Year 15

This measure may be implemented in conjunction with the data scheduled to be collected with the Demonstration Project.

Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 28

Sediment Removal Associated with Water Conservation Measures

CM16: To ensure that significant noise impacts do not occur to native birds, a construction noise minimization program will be implemented. If needed, portable acoustical panels will be placed around the perimeter of the sediment storage site and around the work area to further reduce construction noise.

CM17: Prior to the start of grading activities in the sediment storage site and portion of the haul route that is outside of riparian vegetation, focused gnatcatcher surveys will be conducted to determine the presence of gnatcatcher territories. • Surveys will include the identification of nearby habitat that gnatcatcher may move to or utilize once construction activities start. The qualified biologist will report on whether this nearby habitat is already occupied by gnatcatcher. • Surveys shall also be conducted three days before the start of grading to determine if individual foraging gnatcatcher are present. • Additional nesting season surveys will be conducted annually through the duration of sediment removal activities. • Results of pre-construction, nesting, and pre-grading surveys will be reported to the Service in a quarterly report.

CM18: Excavation and dredging will be conducted between September 16 and January 15. Excavation and dredging may begin in the month of August provided the area is surveyed by a Service-approved qualified biologist in advance and no native fish are present and no larval fish have been observed immediately upstream based on a pre-construction survey. Sediment removal activities may extend until February 14 if larval fish surveys are conducted upstream of the sediment trap by a qualified biologist following the guidelines outlined in CM18 to ensure no native larval fish are present.

CM19: A qualified biologist will be present to monitor sediment removal operations. A qualified biologist is defined as an individual that holds a current 10(a)(1)(A) recovery permit for sucker. This individual or any other project biologist can stop sediment removal activities at any time if impacts to native aquatic species are observed. If impacts to Santa Ana Sucker occur, the Service will be contacted immediately to determine if additional measures to further minimize project impacts are needed or if re-initiation of consultation is necessary. Sediment removal will not proceed until the Service is contacted and a determination is made on how to proceed. The qualified biologist will prepare weekly reports describing the sediment removal activities. These reports will: • Document any sucker observed in the sediment removal channel. • Document behavior of any fish observed in the project area, not only sucker, before and during sediment removal activities. • Record the circumstances and numbers of any fish observed to be wounded or killed during sediment removal activities. Any sucker killed or found dead will be preserved in 95 percent ethanol and submitted to an approved depository.

Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 29

CM20: Floating dredge equipment and heavy construction equipment operating in the wetted channel shall warm up (run idle) for a minimum of ten minutes before initiating the suction dredge to begin removing sediment from the river. During this time the qualified biologist will record observations of any fish in the work area and when complete, but not less than ten minutes after initiating startup noise, will signal the dredge operator to initiate suction dredging activities.

CM21: Prior to and during operation of floating dredge equipment and heavy construction equipment, a spill prevention and contingency plan will be prepared and implemented. The plan will include measures to prevent or avoid an incidental leak or spill, including identification and staging of materials necessary for containment and clean up.

CM22: The configuration of the work area of the sediment trap, conveyance channels and the sediment storage site will allow for wildlife movement when the project is not in operation. Periodic monitoring of the sediment trap and conveyance channel will be performed to ensure the trap does not trap wildlife or become an impediment to wildlife movement.

CM23: Following completion of each sediment removal event (occurring in approximately Year 1, which is anticipated to occur following use by the Alcoa Dike and Demonstration Projects, and Year 25), the sediment storage site will be regraded to its pre-project contours and hydroseeded with native seed to encourage native sage scrub vegetation growth and minimize slope erosion. The sediment removal trap will be revegetated with native riparian vegetation following each sediment removal activity. The access road will remain partially open to facilitate access at a lesser width than the full road between sediment removal years and riparian habitat will be restored along the alignment of the entire access road following the second sediment removal event. These three areas will be weeded for a five-year period following habitat restoration.

PROJECT AREA

Project Region Overview

The Santa Ana River basin is the largest stream system in southern California, with an area of about 2,700 square miles (mi2). The human population of the basin is expected to increase to almost 7 million people by 2025 (Santa Ana Watershed Project Authority 2003). The Project area is regionally located within in southern California in western Riverside County, southwestern San Bernardino County, and Orange County along the Santa Ana River, from about 10 miles upstream of Prado Basin downstream to the Pacific Ocean. The Project area also extends along tributaries of the Santa Ana River: Chino Creek from Prado Basin to an area several miles upstream, and upstream a few miles from Prado Basin along Mill Creek. The upland, wetland, and aquatic areas of the Project area have been heavily modified over the last Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 30 century associated with agricultural activities, water diversions/groundwater pumping, water treatment, flood risk management, and urban development.

The hydrologic and fluvial system of the Santa Ana River and its tributaries have been highly altered, especially in the lowlands. In the mountains, the streams are relatively unaltered except for intense recreational use, including roads and housing, and some diversions for hydropower on the Santa Ana River (Brown et al. 2005). At the transition from mountains to valley, most streams of the basin are diverted directly to public water supplies or are diverted to groundwater- recharge facilities. Groundwater is subsequently withdrawn for various urban uses (Brown et al. 2005). As a result of these far-reaching alterations to the stream systems, streams of the basin including the Santa Ana River generally no longer flow substantially onto the valley floor, except during storm flows that exceed the capacity of the current diversions (Brown et al. 2005). Prior to the changes that accompanied European settlement of the region, the Santa Ana River was a perennial stream that flowed from the mountains to the ocean most of the year (Toupal et al. 2007; Larkin 2015). Two dams on the Santa Ana River, Seven-Oaks Dam and Prado Dam, substantially modify both fluvial processes and water flows in the River, for flood risk management and water conservation purposes.

Santa Ana River

The Santa Ana River originates in the and flows through San Bernardino, Riverside, and Orange counties on its way to the Pacific Ocean. The River, naturally perennial and currently artificially intermittent over much of its length, currently transports more than 125 million gallons per day of released wastewater from Riverside and San Bernardino counties that is utilized for recharge into the Orange County Groundwater Basin; this recycled water satisfies approximately 40 percent of Orange County’s domestic water demand (Santa Ana Regional Water Quality Control Board 2020). Overall water discharges for the River average 322,000 AF per year, although most of this flow is below ground except during storm events (Hanes 1980). Native vegetation along the River ranges from alluvial scrub to riparian woodland. The largest willow woodland in southern California occurs in the Prado Basin behind Prado Dam (Hanes 1981).

Like almost all southern California rivers, the Santa Ana River drains a semiarid landscape that has been subject to periodic wildfire, extensive population and urban growth, and channel modifications including large dams (Warrick and Rubin 2007). These rivers are recognized to be highly event‐driven, producing the majority of long‐term sediment discharge and sediment flux during brief, intense winter events (Kroll 1975; Warrick and Milliman 2003; Warrick and Rubin 2007). The Upper Watershed of the Santa Ana River (above Prado Dam) drains the steep inland mountains and a flat inland plain, while the Lower Watershed (below Prado Dam) drains the lower lying Santa Ana Mountains and a portion of the coastal plain of Orange County.

The Santa Ana River Watershed is has been largely channelized, diverted and urbanized; it begins approximately 96 miles away from the coast and contains over 50 tributaries (LAACPP 2013). The primary waterway of the watershed is the Santa Ana River, which is about 700 miles in length with its tributaries. The watershed catches storm water in 2,650 square miles (mi2) of Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 31

mountains, foothills and valleys that it drains. Today the watershed is home to more than 4.8 million residents. The watershed has urbanized rapidly since the mid‐20th century, and the location of this development has largely occurred in lowlands that were previously used for agriculture (Warrick and Rubin 2007).

Water and sediment discharge in the Santa Ana River is dominated by brief runoff events during wet winter storms occurring mostly in December−March. Under current conditions, on average, half of the annual water discharge and roughly 90 percent of the sediment flux to the ocean occurs during just 3 days per year, while the river discharges almost nothing to the ocean during about 70 percent of the time (Kroll 1975; Warrick and Milliman 2003). Some Upper Watershed water discharge is released to the river mouth during larger storms, as Prado Basin reservoir storage is drained during or soon after storm flow events to provide for increased flood risk management reservoir storage and to drain riparian habitats behind Prado Dam (Izbicki et al. 1998). Owing to the high variability of annual precipitation in the Project region, discharge in the Santa Ana River can vary by many orders‐of‐magnitude from year to year and can be exceptionally high during El Niño−Southern Oscillation winters (Warrick and Milliman 2003). Annual and peak water discharge rates during the period of 1968-2001 suggest a 280 percent (±170 percent) increase in total annual water discharge and a 350 percent (±150 percent) increase in peak water discharge with respect to precipitation over that 34‐year record; these changes are strongly correlated with the wildfire and increased urbanization history of the watershed (Warrick and Rubin 2007). Urban population continues to increase in the watershed. This expansion of urban areas has largely been at the expense of agricultural lands such as citrus orchards and rangeland. These types of landscape changes have been shown to induce increases in rainfall‐runoff discharge. Little sediment passes through Prado Dam to the downstream reaches and the ocean due to its high sediment trap efficiency (higher than 95 percent) (Warrick and Rubin 2007).

Management of groundwater pumping and water diversions on the Santa Ana River is performed by dozens of water supply agencies that deliver water to the growing population of the region (Basin Technical Advisory Committee 2015). The water suppliers in the Upper Santa Ana River Watershed (the region upstream of Prado Dam) reportedly plan to meet future demand for domestic water supply in the region through a combination of imported water, groundwater, local surface water, recycled water, and water use efficiency programs (Basin Technical Advisory Committee 2015). By 2035, demand in the region is projected to increase by over 100,000 AF per year and would likely require the continued development of a diverse water supply portfolio to overcome various challenges and uncertainties (Basin Technical Advisory Committee 2015).

Water suppliers in the Upper Santa Ana River Watershed manage for uncertainties such as variability in water supplies, particularly imported water, caused by drought and other reliability concerns such as catastrophic events, environmental protection goals, mandates in the Sacramento-San Joaquin Bay Delta, climate change, water quality, and imported water costs (Basin Technical Advisory Committee 2015). Domestic water demand has required management of local water quality; past industrial and military activities have caused the requirement of groundwater remediation of volatile organic compound (VOC) contamination plumes (Basin Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 32

Technical Advisory Committee 2015). Water quality treatment is also necessary in some areas of the watershed to treat for other contaminants caused by agricultural activities and urban pollutants (e.g., nitrate, perchlorate, pesticides and inorganic materials; Basin Technical Advisory Committee 2015).

The Upper Santa Ana River Watershed region is highly dependent on local water supplies, particularly precipitation stored as groundwater, which provides approximately 54 to 67 percent of supplies during average rainfall years and over 70 percent of supplies during drought years (USBR 2013; Basin Technical Advisory Committee 2015). The water agencies of the region reportedly plan to store as much water as possible in groundwater basins during wet years and then to pump this water from groundwater storage during drought years (termed as conjunctive use; Basin Technical Advisory Committee 2015). Groundwater use in the watershed is projected to increase over the next 20 years (USBR 2013).

For decades, surface water diversions and groundwater pumping have eliminated most of the dry-weather surface flows in the Santa Ana River system between the mountains and Prado Dam (California Regional Water Quality Control Board 1995). Water diversion and groundwater pumping have eliminated or depleted surface base flows to artificially very low levels on most of the mainstem of the Santa Ana River in general and relative to the ecological needs of native aquatic and riparian systems of the River.

As the inland cities of the watershed have grown, wastewater flows into the River have continued to increase (California Regional Water Quality Control Board 1995), until recently. Between 1970 and 1990, the total volume of wastewater released into the River rose from less than 50,000 AF per year to over 130,000 AF per year (California Regional Water Quality Control Board 1995). These wastewater releases to date partially offset some of the losses of baseflow caused by groundwater pumping and surface water diversions in the watershed. Most of the baseflow of the River below Seven Oaks Dam is currently effluent; the mainstem of the River is now effluent-dominated, a rare circumstance outside of the southwestern U.S. (California Regional Water Quality Control Board 1995). Streamflow in the River is reduced when existing effluent discharges are reduced or removed from the stream system (e.g., as has been increasingly occurring for additional treatment and water supply reuse); beneficial uses can be adversely affected by diversions of wastewater effluent away from the River, including wildlife habitat (California Regional Water Quality Control Board 1995). Table 3 below provides examples of past and projected groundwater pumping and water diversions from the San Bernardino Groundwater Basin Area, a large groundwater basin within the Upper Santa Ana River watershed, in AF per year (Basin Technical Advisory Committee 2015). Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 33

Table 3. Projected Local Water Diversions and Groundwater Extractions in AF per Year, from the San Bernardino Groundwater Basin Area within the Santa Ana River Watershed, by Water Agency10

San Bernardino Groundwater Basin Area Water Agencies, with Water 2015 2020 2025 2030 2035 Demand in Acre-Feet per Year listed Colton, City of 7,000 6,783 6,994 7,408 7,991 East Valley Water District 26,786 28,312 32,150 36,042 39,992 Fontana Water Company 15,100 15,100 15,100 15,100 15,100 Loma Linda, City of 6,814 6,418 6,814 7,236 7,683 Marygold 1,500 1,500 1,500 1,500 1,500 Meeks and Daley Water Company 7,800 7,800 7,800 7,800 7,800 Muscovy 2,100 2,100 2,100 2,100 2,100 Redlands, City of – Municipal Utilities and 33,209 32,109 33,266 34,549 34,549 Engineering Department Regents of California 500 500 500 500 500 Rialto, City of 8,700 8,000 8,000 8,000 8,000 Riverside Highland Water Company 5,100 5,945 7,210 7,950 7,950 Riverside Public Utilities11 59,626 61,626 61,626 61,626 61,626 San Bernardino Municipal Water District 50,233 52,671 54,730 56,866 59,082 Terrace Water Company 900 900 900 900 900 West Valley 17,500 20,500 25,500 28,500 30,500 Other/Private 19,900 19,600 19,300 19,000 19,000 Total Groundwater and Surface Water 262,768 270,864 283,490 295,077 304,273 Demand Safe Yield 232,100 232,100 232,100 232,100 232,100 Extractions above Safe Yield 30,688 38,764 51,390 62,977 72,173 Return Flow from Extractions above the 11,040 13,955 18,500 22,672 25,982 Safe Yield12 Replenishment Obligation13 19,628 24,809 32,890 40,305 46,191

Prado Dam and Prado Basin

The primary purpose of Prado Dam is to provide flood risk management (through regulation of winter stormflow) benefits to the region (Warrick and Rubin 2007). Prado Dam’s basic construction was completed in 1941. The Corps owns and controls Prado Dam, which has a

10 Table re-created from Basin Technical Advisory Committee 2015 11 In 2015, the Riverside Public Utilities reportedly planned to recharge 2,000 AF of water in the Bunker Hill Groundwater Basin and by 2020 they planned to recharge 4,000 AF through the Seven Oaks Dam Conservation Project. Production from the Bunker Hill Groundwater Basin included 4,200 AF of water owned by Western. 12 The Western Watermaster assumes a 36 percent return flow from extractions above the safe yield. 13 The Replenishment Obligation is the Extractions above the Safe Yield minus the Return Flow from the extractions above the Safe Yield. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 34 spillway elevation of 543 ft. Prado Dam traps discharge from 1490 mi2, or 88 percent of the Santa Ana River watershed (Warrick and Rubin 2007).

A secondary beneficial use of the Dam and Prado Basin is water conservation. Water conservation benefits provided by the Dam are possible by the Corps using the Dam structure/operations and Basin area to capture and hold portions of storm flows. The Corps operates the Dam according flow release schedule within an operations manual which generally allows for water to be captured and subsequently released from the Dam at rates which can be captured and recharged in downstream groundwater recharge operations by OCWD (Santa Ana River Watermaster 2011).

The momentary water conservation volume afforded by the Dam is controlled by the allowable WSE during the flood season and non-flood season (March through September). Currently, the maximum water conservation elevation is 498.0 ft. during the flood season and 505.0 ft. during the non-flood season (Scheevel 2015), with a temporary (5-year) deviation to “year-round” elevation 505.0 ft. that would otherwise expire in 2023.

Pursuant to the Corps’ operations manual for the Dam, flood risk management operations at Prado Dam take precedence over water conservation objectives. An elevation of 490.0 ft. is typically the minimum flood season WSE that is held by the Corps during the early stages of a storm event (Scheevel 2015). This WSE is referred to as the “Debris Pool” for the Dam. The Debris Pool is necessary to help limit the amount of floating debris that enters the Dam outlet gates, which in turn helps ensure the gates can function properly during a storm event. Once the Basin has been drained after the last storm event of the flood season, the WSE is typically very near the streambed elevation at the Dam, approximately elevation 470.0 to 474.0 ft. At that time, the Dam water outflow is normally equal to the Prado Basin water inflow (see Figure 2 below). The range of flow rates where inflow is equal to outflow are considered to be the “base flow” condition for the Dam, with modern inflows/outflows typically ranging between 50 cfs to 200 cfs (Scheevel 2015).

In 1995 the Corps and OCWD reached an agreement to increase the seasonal water conservation pool from elevation 494 to elevation 505 ft. after March 1 of each year; in association, OCWD provided funding for control of a non-native plant, giant reed grass (Arundo donax; Arundo) in portions of the watershed (Santa Ana River Watermaster 2011). In 2006 the Corps and OCWD signed an agreement to increase the winter conservation pool elevation in Prado Basin from elevation 494 to 498 ft; in association with this agreement, OCWD contributed to ecological enhancement and restoration in the watershed (Santa Ana River Watermaster 2011).

Prado Dam traps substantial quantities of sediment; nearly all of the sediment that enters Prado Basin with stream water inflows is deposited in the Basin, regardless of the Basin WSE (Scheevel 2015). The sediment removal efficiency of the Basin (as it relates to outflows from the Dam) has been estimated to be greater than 95 percent (Warrick and Rubin 2007).

One of the variables that affects the sediment deposition along the portion of the Santa Ana River upstream of the Basin (e.g., within the first 2.5 miles upstream of the Dam) is the WSE in the Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 35

Basin (Scheevel 2015). It is the large flow events on the Santa Ana River, the effective discharge14, that are the events that likely transport the majority of the overall sediment volume that enters into the Basin over a decades-long period of time (Hamilton et al. 2015; Scheevel 2015). A relatively narrow range of runoff events typically perform the bulk of the sediment transport and channel shaping in a stream over a century (Zeedyk and Clothier 2015). Unlike humid-region rivers, moderate discharges of intermediate to high recurrence (higher frequency storms) probably do not carry the majority of the sediment load on rivers such as the Santa Ana River (Stillwater Sciences 2011; Scheevel 2015). Nevertheless, the relatively moderate (stormflow) water discharge events in the River do move substantial amounts of sediment into the Basin.

-r-- -.r,,.,..-.------..-,,.... nn ... ------,---,--~ 02 04 06~------~ 530..------, 525 520 l"I j 515 _, R£ f.R\OIR _s 510 ~ 505

40 0..------, 3 000 30000 -;;- 25000 ~ 20000 1 15000 u. 10000 5000 o..&....i-,,,,,r'.~~_,1.~ 111£;:~~~~--r-~~~~~-~~ ..=OQ-._.....,...,.-_.i 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Jan2005 - MOUUHA.llrlil ·w,cioMo- u - 01/!J',Jl'lt

Figure 2. January 2005 Prado Dam/Basin Data. (Corps 2005).

14 The effective discharge is a geomorphic concept representing that flow, or range of flows, that transport the most sediment over the long term (USDA 2020). Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 36

BACKGROUND

Alterations in land use, hydrology, fluvial processes, and stream morphology have had significant impacts on ecological conditions in and along the Santa Ana River. Terrestrial natural communities/habitats have been converted to urban land uses. Native riparian vegetation on the River has been removed or extensively altered. The natural seasonal and annual variations in streamflow have been extremely disrupted. Contaminants, such as pesticides, are now commonly found in both surface and groundwater (Brown et al. 2005). These changes have led to declines in populations of various native biota, including aquatic species.

RIPARIAN SYSTEMS

Riparian15 ecosystems are transitional ecosystems occurring between terrestrial ecosystems, where hydrology has little influence, and aquatic ecosystems, where hydrology has a very significant impact on ecosystem function and formation (Gregory et al. 1991; Naiman et al. 1993). Riparian areas provide linkages between water bodies and adjacent uplands and include portions of terrestrial ecosystems that significantly influence exchanges of energy and matter with aquatic ecosystems (NRC 2002). As ecotones, they encompass typically sharp gradients of environmental factors, ecological processes, and plant communities (Gregory et al. 1991). Riparian areas are the land areas that encompasses the river channel outside of the aquatic zone and its current or potential floodplain. Boundaries of riparian zones extend outward to the limits of stream flooding and upward into the canopy of streamside vegetation.

The riparian zone is characterized by a unique set of physical ecological factors in comparison to the surrounding regional landscape (Gregory et al. 1991). These factors include episodic flooding by the stream/river, typically rich and productive soils, a water table that is within reach of dominant plant roots, and species of plants and wildlife that are adapted to the timing of fluvial events such as flooding, drought, sediment transport, and channel movement/migration. This dynamic set of influences creates a wide variety of growing conditions for riparian plants, and over time they develop into various structural forms (typically forests, woodlands, shrublands, meadows, and grasslands) across the floodplain. The heterogeneity of riparian forests/woodlands creates numerous habitat features that explain why riparian forests/woodlands in California support a greater diversity of wildlife than any other natural community type (Smith 1980). Riparian vegetation along river channels also functions as the primary regional movement routes for most large wildlife species.

Riparian systems are complex and composed of interconnected physical (i.e., water and sediment) and biological (i.e., fauna and flora) compartments (Corenblit et al. 2009). Hydrogeomorphic disturbances, such as variability of water flow and sediment erosion, transport and deposition help create a shifting mosaic of physical landform patches and associated aquatic and terrestrial ecological communities along longitudinal and transverse gradients within riparian

15 Riparian: pertaining to the banks and other adjacent terrestrial (as opposed to aquatic) environs of freshwater bodies, watercourses, estuaries, and surface-emergent aquifers (springs, seeps, oases), whose transported freshwaters provide soil moisture sufficiently in excess of that otherwise available through local precipitation to potentially support the growth of mesic vegetation. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 37

corridors (Poff et al. 1997). These complex gradients are crucial for the fundamental biogeochemical functions related to the production of organic matter, water and storage, and water and nutrient cycling, as well as biodiversity (Ward et al. 2002; Naiman et al. 2005).

In the semi-arid environment that characterizes most of southern California, the narrow riparian strip of moist soil bordering watercourses supports the very high abundance and variety of plant and animal life. Less than 10 percent of the California’s original riparian vegetation remains, and over half of this remnant forest and woodland has been heavily degraded (Warner and Hendrix 1984). Water diversions have removed large amounts of water from the streams and rivers of origin, typically greatly modifying their character. Similarly, water impoundments have also greatly modified riparian systems through extended inundation periods. Riverine ecosystems are generally unique, supplying habitats for animal and plant species that are narrowly restricted in their requirements.

Approximately 502 species and subspecies of land mammals are native to California, and 25 percent of those (133 taxa) are limited to or largely dependent upon riparian systems (Williams and Kilburn 1984). Of the 120 species of reptiles and amphibians known to occur in California, half of the reptiles and three-fourths of the amphibians are closely associated with riparian situations (Williams and Kilburn 1984). Native California fishes are typically sheltered by streamside vegetation and obtain much food from the insects that live on the banks and indirectly from the leaves and woody materials provided by riparian vegetation (Warner and Hendrix 1984).

Riparian ecosystems support people as well as wildlife. Rivers and their floodplains provide many “river services” to the surrounding local community. These include: conveyance and delivery of water supply, effective conveyance of flood waters, maintenance of wildlife habitats and regional migration corridors, and recreation opportunities. River services are optimized when a river and its floodplain are healthy. Healthy rivers are normally free of intensive regulation such as dams and bank revetments, and their floodplains support a mosaic of plant communities.

In coastal southern California, riparian corridors occur in a landscape mosaic comprised of human land uses (mainly urban and suburban development) interspersed among limited undeveloped areas, primarily native shrublands. Riparian natural community composition typically reflects larger-scale environmental conditions, such as surface and groundwater availability and stream order, as well as other variables associated with elevation, and/or regional-scale disturbances, such as dams and enhanced atmospheric deposition of nitrogen (Oneal and Rotenberry 2008).

Riparian systems of southern California are naturally patchy and/or isolated (Zedler 2003); however, habitat loss due to anthropogenic factors (e.g., development, dams, groundwater pumping) has further decreased connectivity and destroyed historical wetland complexes (Bauder and McMillan 1998). Low-elevation riparian sites in southern California are usually affected more heavily, while high-elevation sites are somewhat protected due to their lack of accessibility (Stephenson and Calcarone 1999). Heavily altered riparian systems of southern Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 38

California have a reduced capacity to support native fauna and flora and are more susceptible to invasive species (Stephenson and Calcarone 1999).

Within the arid and semi-arid regions of southern California, riparian habitats are very sensitive to changes in the amount, source, and duration of water within a system, which can alter hydrologic and flooding regimes (Poff et al. 2002; Winter 2000; Zedler 2003). Habitats that rely solely on precipitation are the most sensitive to changes in the amount or timing of rain and snow, while groundwater-dependent systems may be less immediately responsive to changes (Poff et al. 2002; Winter 2000). Drought and high-rainfall conditions have widespread effects on riparian system types, and they may shift species composition towards vegetation that can tolerate drier or wetter conditions, respectively. Almost all riparian systems in southern California are adapted to periodic flooding. The dynamic aspect of the native riparian vegetation typically allows for relatively fast recovery from natural flooding disturbance, as long as the natural water flow and sedimentation regimes are intact (USFWS 1998). Episodic heavy flooding events often cause substantial denudation and fluvial erosion-transport-sedimentation that periodically alter structure and function of habitats and reset seral stage age-classes of riparian natural communities. Low-gradient riparian natural communities of southern California provide a variety of ecosystem services, including biodiversity, water supply/quality/sediment transport, recreation, carbon sequestration, nitrogen retention, and flood and erosion risk management.

AQUATIC SYSTEMS

For aquatic systems of southern California, the most ecological information exists for fishes (Brown et al. 2005). Populations of anadromous Pacific lamprey (Lampetra tridentata) and southern California coast steelhead16 (Oncorhynchus mykiss) have been extirpated from most southern California streams (Swift et al. 1993). Native freshwater resident fish species have also drastically declined in the Project region, including Pacific brook lamprey (Lampetra pacifica) (likely extirpated), prickly sculpin (Cottus asper), threespine stickleback (Gasterosteus aculeatus), arroyo chub (Gila orcuttii), speckled dace (Rhinichthys osculus), and Santa Ana sucker (Catostomus santaanae) (Swift et al. 1993; Brown et al. 2005).

The Santa Ana sucker life history illustrates many of the important aquatic features and issues affecting streams of the Project region, including the Santa Ana River. The Santa Ana sucker is a benthic fish that depends on the availability of gravel and cobble substrate for both feeding and spawning (Greenfield et al. 1970). Because adult and juvenile Santa Ana suckers primarily feed by scraping algae from hard substrates, they prefer well-lit reaches with clear water and coarse substrates, where photosynthetic algae can grow (Haglund et al. 2003; Feeney and Swift 2008; Haglund et al. 2010).The water volume and flow of the river plays an important role in shaping its habitats. At times of high river flow, new sources of gravel and cobble are mobilized/distributed along the river, reshaping the channel and creating the complex habitat needed to support all life history stages (i.e., open sandy bars for fry and undercut banks and runs

16 This distinct population segment includes naturally spawned anadromous steelhead (Oncorhynchus mykiss) originating below natural and manmade impassable barriers from the Santa Maria River to the U.S.-Mexico Border (NOAA Fisheries 2020). Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 39 for adults) (USFWS 2017). As flows recede, sand and silt continue to be winnowed from the gravel and cobble, creating conditions suitable for spawning.

Adult and juvenile Santa Ana suckers show a strong preference for bottom velocities less than 1 foot/sec, water depths greater than 10 inches, and coarser substrates including gravel, cobble and mixtures of gravel or cobble with sand. Larvae in tributaries to the Santa Ana River were observed along the edge of the streams in proximity to emergent vegetation, in depths from 1 to 4 inches where the flow was negligible and the bottom was silty (Haglund et al. 2002). Substrate collected from two spawning locations in tributaries to the Santa Ana River included mainly gravel sized particles ranging from 0.03 to 1 inch (Haglund et al. 2001).

Suckers are most abundant in unpolluted, clear water at temperatures that are typically less than 72 degrees Fahrenheit (Moyle 2002). In the Santa Ana River, the Santa Ana sucker is currently dependent on wastewater discharges for its aquatic habitat. Wastewater is typically warmer than naturally occurring river flows and may have increased levels of regulated and unregulated contaminants (USFWS 2017). Saiki et al. (2007) found that overall fitness (body size, weight, age, and general conditions) as well as abundance were lower in Santa Ana suckers found in warmer waters (in the Santa Ana River) relative to those found in cooler waters (in the San Gabriel River). They attributed the reduced fitness in the Santa Ana River to presumed higher metabolic requirements associated with higher temperatures and inadequate food supply (periphyton and insects) in the shifting sand substrate. Mortality of Santa Ana suckers was observed when water temperatures became elevated in the Santa Ana River (water temperature ≥ 91.0 degrees Fahrenheit) during summer 2010 (SMEA 2010). Riparian vegetative cover likely helps to cool the water during the warmer months (Swift 2001a). Similarly, areas of groundwater upwelling provide cool water refugia when present (Feeney and Swift 2008).

Aquatic habitat within Prado Basin (below the OCWD diversion channel at the upstream end of the Basin) is generally unsuitable for Santa Ana suckers when water is pooled behind the dam because Santa Ana suckers avoid standing water (Swift 2001a). As the pool is drained and stream channels form, the aquatic habitat within Prado Basin becomes more suitable, and Santa Ana suckers may enter or be washed into (i.e., in the case of fry) the channels. Baskin and Haglund (2008) collected 15 Santa Ana suckers ranging from 40 to 70 millimeters in the old approach channel to the dam prior its relocation. Although the section of Santa Ana River below Prado Dam has a large, coarse substrate, it has poor water quality (high turbidity) relative to native fish habitat requirements. It also has large numbers of non-native predatory fishes and may have limited habitat for Santa Ana sucker juveniles. Because Santa Ana suckers have not been detected for the last 10 years in this area, and because the range of the species below Prado Dam is isolated from the upstream population, we consider the species currently extirpated from its former range below Prado Dam.

The primary threat to Santa Ana sucker is range-wide modification, fragmentation, and loss of habitat through hydrological modifications. The key challenge to recovery of the Santa Ana sucker and other native fish in the Santa Ana River will be developing a recovery strategy that can be implemented in consideration of the continuing water needs of people in the region and the requirements for flood damage reduction operations to maintain human health and safety. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 40

The remaining isolated population in the Santa Ana River has very limited ability to avoid habitat areas degraded by hydrologic modifications, reduced water quality, invasive plants, and predatory animals. Considering these conditions, they are also now particularly vulnerable to stochastic events, such as wildfire, severe flooding, or a chemical spill, because they have very limited access to tributaries that could provide a refuge during or following such events. Moreover, the small size of the population reduces genetic exchange, which may result in decreased fitness.

Rainfall Patterns and Sediment Movement

On average, California’s coastal watersheds receive 82 percent of the annual precipitation between November and March (National Climate Data Center 2019; Willis and Griggs 2003). As a result, the vast majority of fluvial sediment is moved downstream during storms over these winter months. This imbalance in precipitation results in a regional gradient in average daily water discharge in streams. Peak discharges tend to occur during January, February, and March when watershed soils have reached saturation and subsequent additional rainfall is translated directly into run-off. This seasonal pattern of rainfall and streamflow is heightened by infrequent, exceptionally wet years when large floods flush enormous quantities of sediment out of coastal watersheds. A study of major rivers in Central and southern California has shown that sediment discharge during flood years like 1969, 1983, or 1998 averages 27 times greater than during drier years (Inman and Jenkins 1999).

California’s coastal rivers have exceptionally high sediment loads due to the steep topography, the geologically young and tectonically active terrain, and, in central and southern California, the relatively sparse vegetative cover. Sediment yield, the volume of sediment delivered per square mile of watershed, is typically very high in California relative to other major hydrographic regions of the United States.

Natural Flow Regime

The natural range and variation of flows that occurred over recent historical time on the streams of the western U.S. is referred to as the natural flow regime (Richter et al.1996; Poff et al. 1997). This flow regime sets a template for contemporary ecological processes (Resh et al. 1988; Doyle et al. 2005), evolutionary adaptations (Lytle and Poff 2004), and native biodiversity maintenance (Bunn and Arthington 2002). In riparian ecosystems of arid regions, flow regime drives physiological drought and inundation stresses and physical flooding disturbance (Naiman et al. 1993; Lytle and Poff 2004; Stromberg et al. 2007). Gradients of disturbance and water availability/inundation strongly determine the composition and location of vegetation communities in riparian ecosystems (Pockman and Sperry 2000; Sluis and Tandarich 2004).

Vegetation encroachment, streamward expansion of xeric communities (terrestrialization), and reduced recruitment of some plant species commonly occur in riparian ecosystems of southwestern North America following changes to flow regimes (Turner and Karpiscak 1980; Shafroth et al. 2002; Merritt and Bateman 2012), outside of the typical flow changes that occur within reservoirs behind dams (Nilsson and Berggren 2000; Volke et al. 2019). Flooding, Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 41

inundation, and water stress influence riparian community-level traits (Kyle and Leishman 2009; Hough-Snee et al. 2015).

Altered Fluvial Processes, Geomorphology17, and Hydrology

Sediment is delivered to the river and stream channel by basin erosion processes including hillslope creep, overland flow, landslides, and debris flows. Once delivered to the channel, sediment is transported down the channel network as dissolved or solid load. Solid load, the dominant mode of fluvial transport in California, includes both suspended sediment—sediment that it is fully entrained in the moving water column—and bedload—coarser material that rolls or bounces along the stream bed (California Department of Boating and Waterways and State Coastal Conservancy 2002). About 85 to 95 percent of all sediment is carried as suspended load; however, only 10 to 38 percent of this sediment is sand-size material (California Department of Boating and Waterways and State Coastal Conservancy 2002). Bedload, which typically ranges from 5 to 15 percent of the total sediment load (Collins and Dunne 1990; Inman and Jenkins 1999), is comprised almost entirely of sand- or larger-size sediment. The amount of sediment in transport at any given time depends on both the magnitude of stream flow and grain size of sediment present on the streambed. Natural flow and sediment regimes of floodplain rivers around the world have been changed by river regulation and land management, altering the ecological processes structuring riparian plant communities (Lowe et al. 2010).

Flooding regimes are currently substantially modified in almost all southern California rivers due to upstream dams. Water flows in the Santa Ana River mainstem are substantially controlled or regulated by the operations of Seven Oaks Dam and Prado Dam. In particular, the dams temporarily impound and reduce runoff during storm events and are partially operated for water conservation. These structures do not regulate tributary flow into the river mainstem between Seven Oaks and Prado. Non-storm water flows (baseflow) in the mainstem are greatly influenced by water diversions, groundwater pumping, and groundwater recharge occurring below Seven Oaks Dam.

Seven Oaks Dam is located at the foothills of the San Bernardino Mountains and was constructed in the late 1990s. Prado Dam is located just west of where the river cuts through the Santa Ana Mountains. The Water Resources Development Act (WRDA) of 1986 authorized construction of Seven Oaks Dam and modifications to Prado Dam as part of the Santa Ana River Project (SARP). Cumulative modifications to the hydrologic system in the Santa Ana River from implementation of the SARP have diminished the frequency and extent of channel shaping flow events and interrupted the transport of coarse sediment from the headwaters to the ocean.

The existing dams and diversions on the Santa Ana River have affected the river’s geomorphology primarily through the interaction between sediments, riparian vegetation, and the dam-altered stream flows. Prior to the development of the Seven Oaks and Prado dams and water diversions in the Santa Ana River system, floodwaters would periodically knock down or denude portions of the established riparian vegetation on stream banks and gravel bars. Large amounts of

17 Geomorphology is the study of the nature and origin of the earth's topographic features.

Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 42

sediment would move downstream from the watershed, predominately during larger winter flows. This sediment would deposit on riffles and bars of the River, providing/maintaining fish spawning habitats. Sediment would also move downstream during recurrent flood events and periodically deposit on floodplains, creating new seed beds for vegetation such as cottonwoods and open areas for successional riparian growth. These infrequent storm events episodically denuded portions of the older streamside vegetation areas and rejuvenated riparian scrub, woodland, and forest areas. The operations of Seven Oaks and Prado dams by design have removed the larger flood peaks from the hydrograph of the Santa Ana River. As a result, in areas where (close to the surface) groundwater and/or surface water still exist for most of the year, riparian vegetation has largely encircled (and in some places narrowed) the active channel and covered channel bars and riffles that formerly otherwise would likely typically remain unvegetated. The removed large flood peaks have reduced available native fish habitats and largely eliminated exposed gravel bars from the channel surface in the remaining perennially- wetted channel areas of the River.

Natural high scouring flood flows are greatly reduced or eliminated from the portion of the River below Seven Oaks Dam. Seven Oaks and Prado dams also affect the natural movement of sediment by trapping essentially all of the sediment bedload material and much of the suspended material that formerly naturally moved down the River. The River downstream of Seven Oaks and Prado dams is starved of sediment for a considerable distance, resulting in the degradation of the channel morphology, incision and narrowing, armoring of the bed and banks, and washing away of finer material and riffles, leaving most areas too coarse for Santa Ana sucker and other native fish to spawn on.

On the river substantially downstream of Seven Oaks Dam, the effective removal of most natural high flushing flows, and the artificially slowed river flows upstream of the reservoir pool and sediment deposits behind Prado Dam combine to result in the channel deposition of fine sediments. These fine sediments come mostly from tributaries to the River downstream of Seven Oaks Dam as well as historical sediments in the Santa Ana River floodplain. These fine deposits on and near the channel surface (sand and smaller size sediments) upstream of Prado Basin degrade or eliminate the essential gravel habitats for Santa Ana sucker and other native fish in the severely limited areas with remaining reliable perennial surface water (i.e., the areas downstream of wastewater releases) on the River mainstem.

Seven Oaks Dam Operations

Seven Oaks Dam was anticipated to significantly reduce the amount of sediment moving downstream because it reduces peak flows and traps incoming sediment load (Corps 1988a). A reduction in the transport of coarse sediment (cobble and gravel) to areas occupied by Santa Ana sucker can limit the extent of spawning and foraging habitat available for the species. Wright and Minear (2019) confirmed that Seven Oaks Dam reduced sediment transport capacity near Rialto Drain (i.e., near the upper extent of the range of the Santa Ana sucker) by 20 to 30 percent and deposition rates by an average of 42 percent (across a range of modelled flows from a 2-year to 100-year event). The ability to transport cobble and larger particles was reduced the most, followed by gravel and then sand. Despite the reduction, a significant change in the composition Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 43 of the substrate near Rialto Drain is not anticipated. Cobble and gravel are still anticipated to be deposited due to contributions of sediment from tributaries to the Santa Ana River (Mill Creek, Lytle Creek and to a lesser extent, City Creek).

The regulation of flows at Seven Oaks Dam significantly limits peak flows events. For example, the 10-year frequency flow is anticipated to be reduced from about 8,800 cfs to 500 cfs, which is about half of the pre-Seven Oaks Dam 2-year frequency event (Corps 1988a). In addition to supplying course sediments, periodic flooding can improve habitat for Santa Ana sucker, by reshaping the channel meanders to create the complex habitat needed to support all life history stages (e.g., open sandy bars for fry and deep, undercut banks for adults) (USFWS 2017). In the absence of flows sufficient to reshape the channel, riparian vegetation begins to stabilize the banks, the channel narrows and straightens, and microhabitat features preferred by Santa Ana suckers are further reduced. As the riparian vegetation matures, the canopy covers the narrowed channel reducing the light available for algae production and limiting Santa Ana sucker foraging resources. Although the dam has been operating for many years, changes to stream morphology have not been fully realized because there have been several large releases made, primarily for the purpose of testing the dam outlet structure.

Seven Oaks Dam operations include occasional larger flow releases in association with outlet testing and for environmental purposes (USFWS 2002, 2010). To date, these releases have occurred primarily during the Santa Ana sucker spawning season due to restrictions on operations. As a result of the operational restrictions, future high flow releases are expected to occur outside of the period when high flows would occur naturally (Humphrey 2004) and cannot currently be timed to coincide with tributary flows. High flow releases during the Santa Ana sucker spawning season (which typically follows the storm season) can be energetically costly for adult suckers if they are washed downstream and then must migrate back upstream to suitable habitat before they can spawn. In addition, if eggs, larvae, or juveniles are present during a high flow release they can be washed downstream and perish. If eggs are not washed downstream, they may be buried under sediment that is deposited once flows recede.

Releases from Seven Oaks dam can improve habitat for Santa Ana sucker but should be carefully evaluated to determine the duration and extent of flows necessary to meet the specific objectives of improving habitat conditions (e.g., Wilcock et al. 1996). Timing of the releases with tributary flows during the winter months could reduce the extent of flow required to reshape the channel and would avoid impacts to Santa Ana sucker during the breeding season. In addition, releases made during winter months following initial rainfall events, when the ground is saturated, could reduce the amount of percolation that occurs between Seven Oaks Dam and the reach below Rialto Drain.

Prado Dam Operations

Prado Basin receives an estimated 1,200,000 yd3 of sediment annually (about 0.5 to 0.7 ft. over the basin area) and nearly all of this sediment is deposited in the basin proper (Scheevel Engineering 2015). As much as 40 ft. of sediment has deposited along the Santa Ana River, including as much as 12 ft. near Hamner Avenue, since the dam was constructed (DEIS, Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 44

Appendix K, page 10). Despite the significant cumulative deposition, the slope of the streambed between Prado Dam and Hamner Avenue has remained about the same (about 0.003) since the dam was constructed (Scheevel Engineering 2018). We attribute the lack of change in slope to successive increases in the elevation of the outlet sill since 1941.

Modifications completed on Prado Dam in 2008 included raising the dam 28.4 ft. and the outlet invert 10 ft. (Corps 1988b). As a result of the modifications, the Corps anticipated additional sediment deposition in the future with-project condition (100 year), ranging from about 20 ft. near the dam to 0 ft. near Hamner Avenue, at 563 ft. elevation (Corps 1988b).

The capacity within Prado Basin will continue to be reduced by about 700 AF per year, based on current operations (Corps 2019a, Appendix N). As the capacity of the basin is reduced, incoming storms will fill up the basin faster and water will be held at progressively higher elevations to accommodate safe flow releases to downstream areas. When water is held at a higher elevation, sediment is deposited further upstream and the stream gradient becomes progressively flatter. The sediment that is deposited primarily consists of sand and smaller particles because course material (i.e., gravel and cobble) is substantially captured upstream within Seven Oaks Dam, debris basins, flood damage reduction basins and groundwater recharge facilities (Scheevel Engineering 2018). An increase in fine sediment deposition, combined with a reduction in stream gradient, is anticipated to expand the extent of backwater pools. Backwater pools favor non- native animals, such as largemouth bass (Micropterus salmoides), that are predators on the Santa Ana sucker, and the fine substrate that settles out in still water will not support breeding and foraging habitat for Santa Ana sucker.

Prado Dam has effectively cut off the supply of coarse sediment delivered to the lower Santa Ana River from upstream sources and has greatly altered geomorphic processes and aquatic natural community conditions in the channel and floodplain downstream of the dam. A net loss of about 5,000 yd3 of sediment (on average) is anticipated to be eroded from the Santa Ana River bed downstream of Prado Dam and delivered to the ocean each year as a result of operations enabled by the new outlet (Corps 1988b). Without additional coarse sediment delivery to the channel (from upstream sources), the existing alluvial sediments in the bed and river terraces/bars (including sand and gravel) have decreased as these sediments are transported downstream and not replaced (e.g., see Chang 2003; Fulton 2008; Pasternack 2008). The reduction in coarse sediment supply has been compounded by the armoring of channel embankments along much of Reach 9 as part of the SARP, with the resultant “capping” of alluvial sediments deposited in the former outer floodplain and meander zone of the river. These alluvial sediments would otherwise be available to be mobilized during flood flows and follow the natural meander of the river over time.

The operation of Prado Dam, has, and probably will continue to cause degradation, incision, and narrowing of the channel; reduction of high function spawning sand and gravel for native aquatic species; and reduction of riparian ecosystem functions in the reach below the dam (e.g., see Pasternack et al. 2010). Chang (2008) estimates the channel bed near Prado Dam will be incised by about 26 ft., although a grade control structure at the downstream end of Reach 9, just below Weir Canyon Road Bridge, prevents local degradation of the channel bed in this area (Tetra Tech Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 45

2012). Currently, the channel is incised below the dam and transitions to a wide, shallow run as the river approaches the grade control structure. We anticipate the channel morphology between Prado Dam and Weir Canyon Road Bridge will continue to evolve until the bed becomes armored (i.e., all smaller particles are washed downstream leaving larger substrate in place that cannot be moved by the available flows). The channel morphology in Reach 9 no longer supports Santa Ana sucker. Restoration, including sediment management, will be required to reestablish the complex habitat needed to support all life history stages of the Santa Ana sucker and to reduce the extent of habitats currently available for non-native aquatic species.

Base Flows and Water Quality

Historically, the Santa Ana River flowed perennially throughout its length (McGlashan 1930). However, the withdrawal of ground and surface water for water supply currently de-waters the Santa Ana River below Seven Oaks Dam outside of winter storm periods. Aquatic habitat for Santa Ana sucker is maintained primarily by discharge of treated wastewater effluent, near surface ground water, and non-point urban and agricultural runoff (MEC and Aspen 2000). These water sources have all declined in recent years. Projected future climate changes, and changes in water availability in this region (Hayhoe et al. 2004; Seager et al. 2007; Seager and Vecchi 2010; Dominguez et al. 2012), when combined with the substantial ongoing water diversions and groundwater pumping in the watershed, may further alter river flow management and consequently adversely affect riparian and aquatic natural communities along the Santa Ana River. Annual surface water in the Santa Ana River is likely to decrease over future periods due to climate change (USBR 2013).

Two wastewater treatment facilities provide water to the 2 to 8 mile reach where the mainstem population of the Santa Ana sucker is located. The Rapid Infiltration/Extraction Wastewater Treatment Facility (RIX) discharges water to the river in Colton, about 1.4 miles upstream from Riverside Avenue. The City of Rialto's Municipal Wastewater Treatment Plant (Rialto Treatment Plant) discharges to the Rialto Drain, a tributary that enters the Santa Ana River just upstream from the RIX discharge point. At the time the Santa Ana sucker was listed, discharges ranged from about 60 to 70 cfs of flow from the RIX facility and 10 to 15 cfs from Rialto Drain (Swift 2001b). In 2019, the RIX facility discharged an annual average of about 55 cfs; current discharges to Rialto Drain average about 10 cfs.18

Discharge downstream of the main population of Santa Ana suckers and in tributaries has also been reduced. OCWD’s diversion point near River Road Bridge diverts about 50 percent of the Santa Ana River into the Prado Wetlands for treatment. OCWD reported that flows in the vicinity of the diversion were reduced from about 200 cfs prior to 2009 to less than 60 cfs in 2018 (OCWD 2018). Reductions in tributary flows to the Santa Ana River were observed in Sunnyslope Creek, Lake Evans Drain, and Arroyo Tequesquite (OCWD 2020; Russell et al. 2019). The tributaries are drying up for several months in the summer and no longer connect to

18 Information received from K. Palenscar (San Bernardino Valley Municipal Water District) on April 3, 2020. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 46

the main channel. Reductions in flow are likely associated with water conservation programs and/or implementation of MS4 permit requirements (Russell et al. 2019).19

Reduced base flows are detrimental to the Santa Ana sucker because they reduce the overall extent of habitat (lower flow covers less stream bottom), are subject to greater temperature fluctuations (lower flow is more prone to solar heating), and increase the risk of predation (lower flow reduces the depth of pools) (Swift 2001b). Lower velocities and warmer temperatures create habitat conditions that are more suitable for non-native fish species that may compete or prey on suckers. Reduced velocities associated with lower flows have a reduced capacity to clear fines from the streambed after storm events. Finally, reduced base flows have the potential to percolate into the streambed, eliminating habitat entirely (as has occurred in the tributaries).

Operations of the RIX and Rialto Treatment Plants require periodic shutdowns for maintenance. Discharges to the Santa Ana River are turned off during the shutdowns to prevent exceedances of water quality requirements. An evaluation of a 7-hour shutdown period at RIX in 2003 resulted in a determination that the shutdowns were unlikely to harm Santa Ana suckers because only a small section of habitat, between the discharge pool and confluence with Rialto Drain became dewatered (Allen 2003). Discharges from Rialto Treatment Plant, combined with groundwater levels that were present in 2003 prevented dewatering of the habitat. The current flows from the Rialto plant and current groundwater levels are inadequate to support Santa Ana sucker during shutdowns. The RIX Wells Retrofit Project, completed in late 2017, provides supplemental water to the river during shutdowns to maintain water flows. In absence of the additional flows, the shutdowns were resulting in stranding of hundreds of Santa Ana suckers because surface water flow percolated into the channel bed during the shutdowns (RWQCB 2016). Testing of the efficacy of the supplemental flows during a shutdown event is ongoing. There is still potential for areas occupied by Santa Ana sucker to be dewatered in Rialto Drain due to shutdowns of the Rialto Treatment Plant and in smaller channel braids below the RIX discharge point due to RIX shutdowns; however, efforts to salvage stranded Santa Ana suckers significantly reduced mortality during several events (Russell et al. 2017; Russell et al. 2019). Specific plans to ensure adequate protection of Santa Ana sucker during required shutdowns are under development.

Wastewater-dominated rivers, like the Santa Ana River in its modern condition, are subject to increased inputs of regulated and unregulated contaminants, which degrade water quality and suitability of habitats for many native aquatic species (Kolpin et al. 2002; Jenkins et al. 2009). Contaminants effects in water discharged from sewage treatment facilities are often amplified because of the artificially diverted baseflow of typically cleaner, natural water (from rainfall in the watershed) that otherwise would help dilute residual chemicals (Kolpin et al. 2002; Jenkins et al. 2009). Additive to this, contaminants from urban runoff are also substantial on the Santa Ana River. Degraded water quality likely affects Santa Ana sucker and other native fish species in the Santa Ana River (USFWS 2017). Other water quality impacts to native fish in the Santa Ana River include (but are not limited to): elevated water temperatures, changes in hydrological

19 Municipal Separate Storm Sewer System (MS4) permits are required by the State Water Resources Control Board as part of the Municipal Storm Water Program to reduce the discharge of pollutants from conveyances (roads with drainage systems, municipal streets, catch basins, curbs, gutters, ditches, man-made channels, or storm drains). https://www.waterboards.ca.gov/water_issues/programs/stormwater/municipal. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 47 regime, low oxygen levels attributed to increased nutrients loads causing algal blooms, and increased ammonia levels that are toxic to fish (USFWS 2017). Each of these scenarios may result in degradation of water quality in occupied habitats and elevated stress of native fish, lower reproductive output, or death (USFWS 2017).

Aquatic Invasive Species

Non-native predatory fish (e.g., green sunfish and largemouth bass) were uncommon in the upper part of the Santa Ana sucker’s range above Prado during surveys conducted in 1999 and 2000; high winter flows flushed the non-native fish downstream so that their numbers were lower in the spring when sucker fry were present (Swift 2001a). Flooding can remove/reduce local populations of invasive aquatic faunal species, allowing native species that are more adapted to flooding to recolonize the area (Doubledee et al. 2003; Gamradt and Kats 1996). Invasive species were more common further downstream on the Santa Ana River closer to Prado Basin, where the channel gradient was reduced and backwater habitats were more prevalent. The most common non-native fish species found in this lower portion of the river (above Prado) were fathead minnow, green sunfish, bullheads (Ameiurus natalis), largemouth bass, and mosquitofish (Gambusia affinis) (Swift 2001a).

Conditions for non-native species in the upper part of the Santa Ana sucker’s range have changed substantially. Increased temperatures and reduced velocities associated with the reduction in wastewater discharges have created conditions more suitable for non-native predatory fish. Regulation of water flow at Seven Oaks Dam reduces the frequency and severity of high flow events, contributing to the uninhibited expansion of non-native fish populations. Thousands of non-native fish were removed from Rialto Drain and the river below the RIX annually between 2017 and 2019 (Russell et al. 2017; Russell et al. 2019). For example, in 2017, over 4,600 non-native fish were removed from Rialto Drain, largely mosquito fish and bullhead (Russell et al. 2017). The number of largemouth bass, a known predator on Santa Ana sucker, has increased exponentially since 2017 (Brown et al. 2019). In the absence of a regular non- native fish capture and removal program, and given the limited remaining area of suitable habitat, largemouth bass could decimate the Santa Ana sucker population.

Downstream of Prado Dam, the habitat conditions are generally more suitable for non-native fish than Santa Ana suckers. As described by Aspen (2015): “Nearly all physical characteristics of the Santa Ana River downstream of the Prado Dam favor non-native species over native species. These characteristics include deep slower moving water, warmer water temperatures, increased suspended solids in the water column, and more regulated flows.” Surveys conducted during water diversions for construction of SARP projects captured thousands of non-native fish, including hundreds of largemouth bass (RCRCD 2005, 2010; Aspen 2015).

Inundation

Relatively long-term artificial inundation along streams is now moderately common worldwide behind dams, and is known to have substantial effects on riverine vegetation (Nilsson and Berggren 2000). The relatively novel hydrology caused by artificial extended inundation behind Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 48 dams has relatively little natural correspondence in freshwater systems (e.g., natural lakes) in the western U.S., and hence few native riparian species have effective adaptations to these conditions. To identify different hydrologic influences in backwater environments that form behind many dams, it is important to distinguish between shorter‐term flooding related to fluvial processes from longer‐term inundation related to reservoir fluctuations (Flick et al. 2012; Liro 2019). Differentially, inundation affects riparian areas and the plants and wildlife that can occupy them in variety of ways, associated with the period, depth, frequency (e.g., annually repeated extended inundation), and season of inundation. Inundation tolerance is related to the ability of a plant to develop adaptive structures to cope with the lack of oxygen caused by the excess of water in the soil (Rodríguez and Luquez 2016). Willow and cottonwood (Populus sp.) forest patches along streams rely on periodic natural short-term inundation through over-bank flows for capillary wetting of the soil surface in areas with shallow water tables; this moistens the soil as is necessary for Fremont's cottonwood (Populus fremontii) establishment, rewaters mature trees on higher floodplain landforms, and reduces competing, encroaching (less inundation-tolerant) vegetation (USDA 2003; Hough-Snee and Anchor 2019).

Results of an extended-duration inundation study (USFWS 2008) of 3-year old native plantings in northern California showed that young black willow, Fremont cottonwood, and narrow-leaf willow (Salix exigua) were quite tolerant of the relatively long-duration inundation conditions at low water depths. Young arroyo willow plantings were moderately tolerant of standing water inundation. California blackberry (Rubus ursinus) and California wild rose (Rosa californica) showed relatively low tolerance for extended inundation, but with some variation. Coyote brush (Baccharis pilularis) and blue elderberry (Sambucus mexicana) showed very low tolerance of standing inundation from floodwaters (USFWS 2008).

Throughout western North America, willows and cottonwoods are often dominant woody plants in riparian streamside areas that are naturally periodically inundated (Amlin and Rood 2001). Most native riparian plants species of the Project area are competitively and variously adapted to certain limited periods/cycles of inundation, based on the natural hydrograph of most streams in the southern California.

Black willow, a dominant tree in the riparian areas of Prado Basin and the larger Project area, is quite tolerant of inundation and normally a black willow tree survives frequent and long-term inundation, including reportedly total submersion during the growing season for more than 50 days (Walters et al. 1980); inundation during the dormant season of less than 2 months is expected to have little adverse effects on black willow actual survival. Black willow survival of inundation is high compared to almost all native riparian woody plants on the Santa Ana River (Corps 2019a). Nevertheless, inundation of black willow during the growing season is expected to cause die-back of new growth (i.e., severe reduction of leaf-out below the extended inundation water level), prevent seed establishment, and prevent seedling establishment (Corps 1998); temporary adverse effects to such leaf-out of willow riparian areas is expected with as little as 3 days of inundation during the growing season (USFWS 1990); if foliage is submerged, the foliage leaf-out is lost after 3 - 7 days of inundation and likely unavailable for bird foraging or nest placement during that year’s breeding season when the water recedes (Corps 2019a). Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 49

Cottonwood trees are usually regarded as fairly tolerant to excessive soil moisture, but in general, willows are typically more inundation-tolerant than cottonwoods (Volke et al. 2019), with California sycamore less tolerant of inundation than mulefat or cottonwoods (Soil Conservation Service 1993). This is reflected in natural riparian zones, where willows grow more often in the lower, inundation-prone sectors, while cottonwoods more typically occupy the higher floodplain areas (Amlin and Rood 2001), with sycamores occupying areas even less susceptible to extended inundation. Along streams in the western U.S., the upper elevation limit (relative to the stream water level) of the Fremont cottonwood seedling establishment depends on the proximity of seedling roots to the water table; the lower elevation limit along a stream is a function of the elevation of inundation or scour (Auchincloss et al. 2012). Natural replacement of Fremont cottonwood populations in the riparian corridor is substantially more successful when inundation does not completely cover the shoots of seedlings for more than 2 weeks in a season, and if water temperatures during inundation are cool; Fremont cottonwood seedlings are sensitive to even partial inundation for 2 weeks or more (Auchincloss et al. 2012). Adult cottonwood are reported to have moderate tolerance to inundation and are severely damaged by inundation of 6-10 days (Soil Conservation Service 1993). The following are components of the annual hydrograph generally essential to Fremont cottonwood seedling emergence and growth: 1) flood flows that precede seed dispersal to produce suitable germination sites; 2) inundation recession following a flood peak to expose germination sites and promote seedling root elongation; and 3) stream base flows that supply soil moisture to meet summer and winter seedling water demand (Shafroth et al. 1998; USDA 2003).

Mortality of mulefat seedlings is expected with submersion for 1-2 weeks (Corps 1998). Mature mulefat plants are expected to suffer extensive die back/reduced leaf-out from inundation of 3- 14 days. Depending on the period of inundation, surviving mulefat plants do eventually sprout back from the base; nevertheless, these plants typically do not provide suitable least Bell’s vireo nesting substrate during the nesting season immediately following the inundation events (Corps 2019a). At any particular water inundation depth, mulefat and other native understory shrub and herbaceous species would be more likely to be subject to complete rather than partial inundation due to their shorter heights compared to native riparian tree species.

Backwater Effects

Dammed rivers have unnatural stream flows, disrupted sediment dynamics, and rearranged geomorphologic settings (Aguiar 2019). Behind dams, water reservoirs are superimposed on rivers, and reservoir base level changes affect upstream river reaches that fluctuate seasonally in response to reservoir management as well as over multi‐year wet and dry cycles (Volke et al. 2019). Upstream from dams, the water held behind the dam creates backwater20 effects that typically induce sediment deposition, cause more frequent and higher valley-floor inundation, increase groundwater levels, and change channel morphology and riparian vegetation (Liro 2019). Backwater-induced changes in hydrodynamics21 and sediment transport favor growth of certain classes of plants and decrease their mortality during floods, but also eliminate plants

20 A backwater is a continuum of landforms where sediment accumulates due to the presence of a reservoir. 21 Hydrodynamics is the study of dynamics of fluids in motion. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 50 intolerant to prolonged inundation and intensive fine sediment deposition (Liro 2019). These impacts may change the structure of river system by modifying trajectories of vegetative succession cycles in the river corridor (Liro 2019). Specifically, backwater effects often promote the development of more stable channel morphology and a less diverse mosaic of riparian vegetation and wildlife habitats, contrasting with those occurring in free-flowing rivers of the temperate zone (Liro 2019).

In one study from South Dakota, river base level changes caused by reservoir filling resulted in the thalweg of the lower 19 miles of the original White River channel and adjacent floodplain aggrading by up to 39 ft. between 1954 and 2011 (Volke et al. 2019). The resultant overall channel slope upstream from the reservoir basin flattened from 3.7 to 1.6 ft. per mile.

Environmental Flows

Natural resource agencies and managers are often faced with the complicated task of protecting and restoring a broad suite of ecological functions and public values to rivers while accounting for the existing uses. A good understanding of how instream flow levels and regimes relate to the many beneficial uses, functions, values, and services of rivers (e.g., flood risk management, water supply, biological productivity, species support, etc.), and the scale of alteration from the natural condition, is necessary for informed river management (California Environmental Flows Workgroup 2019).

Instream flows are defined as the volume of water in a stream to adequately provide for instream uses within the stream channel (i.e., aquatic organisms and riverine processes). Instream flows are often divided into ecological flows and environmental flows. Ecological flows are defined as a set of flow metric values necessary to determine a flow regime that sustains ecological endpoints (habitat processes, ecological functions, or species life history stages) within a lotic water body and its margins (California Environmental Flows Workgroup 2019). Environmental flows, on the other hand, are defined as ecological flow prescriptions adjusted to consider and balance other competing human uses to produce a flow regime that balances human and ecological needs (California Environmental Flows Workgroup 2019). The term environmental flows has also been referred to as the component of water flowing down a river that is reserved or released into it, solely for the purpose of improving the ecological environment or managing the condition of the ecosystem, of rivers and their floodplains (King et al. 2003), where competing water uses for that flow exist (Dyson et al. 2008). Environmental flows are also sometimes considered as “balanced” flow levels allowing for hydrologic alteration due to uses other than the environment or ecosystem. However, environmental flows generally mimic patterns of the natural flow regime to achieve desired ecological outcomes (California Environmental Flows Workgroup 2019).

Restoration or enhancement of artificially degraded key stream water flow components will typically improve riparian and freshwater ecosystem health by restoring essential or important physical processes and habitat conditions (UC Davis 2019). Environmental flows generally mimic the important high- and low-flow patterns of the natural flow regime in order to achieve desired ecological outcomes (California Environmental Flows Workgroup 2019). Within Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 51

California, the need for environmental flows has arisen from the high degree of flow regulation and/or water extraction from rivers. It is increasingly clear that, in the mid and long term, failure to meet environmental flow requirements often has dire consequences for river ecosystems and the species that depend upon them. Addressing the water needs of aquatic and riparian ecosystems will often mean reducing the water use of one or more sectors. These are normally tough choices, but are often essential to ensure the long-term ecological viability of river systems (Dyson et al. 2003). Environmental flows do not require restoring the natural, pristine flow patterns that would occur absent human development, use, and diversion but, instead, are intended and needed to produce a broader set of functions and benefits from rivers than from management focused strictly on water supply, energy generation, and/or flood risk management.

From the turn of the 20th century through the 1960s, water management in developed nations predominantly focused largely on maximizing flood protection, water supplies, and/or hydropower generation. During the 1970s, the ecological and economic effects of these projects prompted scientists to seek ways to modify dam operations to maintain certain fish species. The initial focus was on determining the minimum stream flow necessary to preserve an individual species, such as trout, in a river. Environmental flows evolved from this concept of “minimum flows” and later, “instream flows,” which emphasized the need to keep water within waterways. By the 1990s, scientists came to realize/emphasize that the biological and social systems supported by rivers are too complicated to be summarized by a single minimum flow requirement (Bunn and Arthington 2002; Richter and Thomas 2008). Since the 1990s, restoring and maintaining more comprehensive environmental flows has gained increasing support, as has the capability of scientists and engineers to define these flows to maintain the full spectrum of riverine species, processes and services. Furthermore, implementation has evolved from dam reoperation to an integration of all aspects of water management (Dyson et al. 2003), including groundwater and surface water diversions and return flows, as well as land use and storm water management. The science to support regional-scale environmental flow determination and management has likewise advanced (Arthington et al. 2006).

The importance of a river’s flow regime for sustaining biodiversity and ecological integrity is well established (Poff et al. 1997; Hart and Finelli 1999; Bunn and Arthington 2002). Streamflow is viewed as a ‘maestro’ (Walker et al. 1995) or ‘master variable’ (Power et al. 1995) that shapes many fundamental ecological characteristics of riverine ecosystems (Poff and Zimmerman 2010). From a basic ecological perspective, extreme events such as high flows and low flows exert selective pressure on populations to dictate the relative success of different species, and patterns of variation in ‘sub-lethal’ flows can influence the relative success of different species and regulate ecosystem process rates (Resh et al. 1988; Hart and Finelli 1999).

In many regulated river systems, stipulated or required environmental flows provide an important component of the stream flows within the system. In regulated (dammed) rivers, the term environmental flows usually refers to a volume of water that is held in storage and released to the river environment at times designed to benefit natural ecosystem processes (Reid and Brooks 2000). In unregulated streams, the primary source of environmental flows is typically derived from water “savings” that result from reduced water extraction, generally increasing surface low flow levels outside of the rainy season (King et al. 2003). Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 52

Freshwater plants and animals have evolved with, and intimately depend upon, natural patterns of hydrological variability. As inferred above, naturally high and low water levels create habitat conditions essential to reproduction and growth, and drive ecological processes required for ecosystem health. Specific patterns of freshwater flows also support a range of other services provided by river systems. For example, flood pulses move sediment that maintains the form and function of rivers. Seasonal inundation of floodplains and wetlands supports groundwater recharge.

When a river has been dammed, one of the obvious changes is the disruption to the amount and timing of its flow. “Environmental flows” is a system for managing the quantity, timing, and quality of water flows below a dam, with the goal of sustaining freshwater and estuarine ecosystems and the human livelihoods that depend on them. The most ecologically important aspects of a river’s flow are extreme low flows, low flows, high flow pulses, small floods, and large floods. Environmental flows can be designed to restore any of these, with the goal of improving water quality, restoring sediment deposition, addressing the life-cycle needs of fish and wildlife, and restoring the livelihoods of river-based communities.

One effort currently underway to restore environmental flows is the Sustainable Rivers Project, a collaboration between The Nature Conservancy (TNC) and the Corps, which is the largest water manager in the United States. Since 2002, TNC and the Corps have been working to define and implement environmental flows by altering the operations of Corps’ dams in 8 rivers across 12 states. Dam reoperation to release environmental flows, in combination with floodplain restoration, has in some instances increased the water available for hydropower production while reducing flood risk. Arizona’s Bill Williams River, flowing downstream of Alamo Dam, is one of the rivers featured in the Sustainable Rivers Project. Having discussed modifying dam operations since the early 1990s, local stakeholders began to work with TNC and Corps in 2005 to identify specific strategies for improving the ecological health and biodiversity of the river basin downstream from the dam. Scientists compiled the best available information and worked together to define environmental flows for the Bill Williams River (USGS 2006). While not all of the recommended environmental flow components could be implemented immediately, the Corps has changed its operations of Alamo Dam to incorporate more natural low flows and controlled floods. Ongoing monitoring is capturing resulting ecological responses such as rejuvenation of native willow-cottonwood forest, suppression of invasive and non-native tamarisk, restoration of more natural densities of beaver dams, and enhanced groundwater recharge. Corps engineers continue to consult with scientists on a regular basis and use the monitoring results to further refine operations of the dam (Shafroth et al. 2010).

Environmental flows have been required more often in northern California as compared to southern California; in northern California, multiple agencies typically share responsibility for setting flow criteria that protect and improve the ecological health of the State’s water resources (UC Davis 2019). No overall framework or guidance for determining flow criteria in California currently exists. This is compounded by the lack of species-specific hydrograph information and environmental flow data, and the data that are available are difficult to compare across the state. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 53

We are recommending below that the Corps coordinate, partner, develop, and implement environmental flows on the Santa Ana River to sustain and maintain the aquatic and riparian ecosystems that depend on the River. In order to determine appropriate environmental flows, any agency needs to consider the range of pertinent aspects of the river and drainage system in their context (Dyson et al. 2003). This involves evaluating the River watershed from its headwaters to the coastal environments and including its wetlands, floodplains and associated groundwater systems. It also means considering environmental, economic, social, and cultural values in relation to the entire system. A wide range of outcomes, from environmental protection to serving the needs of industries and people, are to be considered for the setting of an environmental flow. To set effective environmental flows, one needs to identify clear objectives as well as water use scenarios. These objectives should have measurable indicators that can form the basis for water allocations. Such objectives and scenarios can best be defined with multi- disciplinary expert teams and stakeholder representatives such as water districts. Defining water flow criteria requires making informed societal choices on water allocations. Much depends on stakeholders’ decisions about the future character and health status of these ecosystems. Scientists and experts can help inform such decisions by providing information and knowledge on how a river will evolve under various flow conditions.

More than 200 methods are used worldwide to prescribe river flows needed to maintain healthy rivers. Some potential relatively comprehensive approaches include DRIFT (Downstream Response to Imposed Flow Transformation; King et al. 2003), BBM (Building Block Methodology; King and Louw 1998), and the “Savannah Process” (Richter et al. 2006) for site- specific environmental flow assessment, and ELOHA (Ecological Limits of Hydrologic Alteration; Poff et al. 2010) for regional-scale water resource planning and management. The most effective methods for a given situation depend on the amount of resources and data available, the most important issues, and the level of certainty required. To facilitate environmental flow prescriptions, a number of computer models and tools have been developed by groups such as the Corps’ Hydrologic Engineering Center to capture flow requirements defined in a workshop setting (e.g., programs such as HEC-RPT) or to evaluate the implications of environmental flow implementation (e.g., HEC-ResSim, HEC-RAS, and HEC-EFM) (Cao and Roberts 2012; Corps 2020).

DESCRIPTION OF PROJECT AREA BIOLOGICAL RESOURCES

More comprehensive descriptions of expected biological resources of the Project area and potential impacts from the proposed Project are found within the Service’s 2020 BO (FWS- WRIV-09B0192-20F0606) on the Project, and is herein incorporated by reference for increased brevity of this Final CAR. Additional descriptions of biological resources in the Project area are found within the Corps’ feasibility study for the proposed Project (Corps 2019a). Past BOs associated with Corps/OCWD requests for water conservation include BO 1-6-95-F-28, issued in 1995 for non-flood season water conservation to elevation 505 ft.; BO FWS-WRIV-2102.3, issued in 2002 for flood season water conservation to elevation 498 ft.; and BO FWS-WRIV- 09B0192-18F0101, issued in 2018 for a 5-year flood season deviation to 505 ft. These past BOs also contain relevant information on the Project area and potential ecological impacts. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 54

Historically, the Santa Ana River and its tributaries traversed unobstructed floodplains and flowed substantially more surface and groundwater compared to today. These channels and floodplains supported diverse and complex systems of riparian corridors, freshwater marsh, and stream aquatic communities (Corps 2019a). These aquatic and riparian systems supported a large variety of wildlife ranging from large mammals to abundant native fish that occupied productive ecological niches along the drainages throughout the Santa Ana River watershed. Only a small percentage of these natural communities and habitats now remain along the River, as a result of water diversion and groundwater pumping (e.g., San Bernardino Valley Municipal Water District 2020; Western Municipal Water District 2004; Santa Ana River Watermaster 2011; Basin Technical Advisory Committee 2015), flood risk management, agricultural conversion, and urban development, as well as proliferation of invasive exotic vegetation and non-native animal species throughout the Santa Ana River watershed (Corps 2019a).

The Santa Ana River is a major drainage that connects coastal regions of Orange County with interior regions of Riverside and San Bernardino counties. The riparian and upland natural communities that occur in and adjacent to the Santa Ana River provide habitats for a variety of resident and migratory wildlife species including several special-status species. The River channel and floodplain provide an important regional linkage of ecosystems from the immediate coastal plain with the interior plains and valleys of the region. The Prado Basin with its extensive riparian woodland/forests provides a very substantial portion of the biological resources within this linkage. River channels in arid regions provide wildlife movement corridors that are essential to many species survival due to the continuous ribbons of vegetation, open movement routes, and nearby water that wildlife use for cover and food that are typically more limited in drier upland habitats (Levick et al. 2008; Corps 2019a). Prado Dam and its surrounding structures reduce or impede upstream/downstream movement of several native species.

The stretch of the Santa Ana River and corresponding floodplain within the vicinity of the Reach 9 portion of the River (downstream of Prado Dam) is somewhat surrounded by a variety of developed land uses. The River channel and floodplain in Reach 9 are the important primary areas of wildlife habitats remaining in that portion of the Project area. The River and corresponding remaining portion of undeveloped floodplain provide a linkage for wildlife, such as mountain lion (Felis concolor), bobcat (Lynx rufus), and American badger (Taxidea taxus), to occupy the River, move up and down the River, and/or move north-south to additional major core ecological areas. These core areas include the Santa Ana Mountains to the south, Prado Basin to the east, and Puente-Chino Hills to the north (Beier 1995; Noss et al. 2002; Spencer et al. 2001). This linkage is highly important, as the Santa Ana Mountains and the Puente-Chino Hills together encompass about 511,000 acres of wildlands containing biological resources of statewide and national importance (Royte 2002; Noss et al. 2002; Hunter et al. 2003). The Chino Hills State Park and Santa Ana Mountains (Cleveland National Forest) are separated by the Santa Ana River Canyon downstream of Prado Dam and Basin; the ecological linkage between these two core areas was historically once several miles wide along the Santa Ana River Canyon in Reach 9 (Noss et al. 2002). The linkage between core areas in the Santa Ana Mountains, Prado Basin, and the Puente-Chino Hills is now narrow and/or tenuous due to the Riverside Freeway SR-91 (this freeway parallels Reach 9 of the River), the Corona Expressway SR-71 (this freeway separates the Puente-Chino Hills from Prado Basin, and associated urban development (Koelle Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 55

2003; Noss et al. 2002; Vandergast et al. 2007; Corps 2019a). The only passageways remaining for non-flying wildlife to safely traverse SR-91 and SR-71 into or out of Prado Basin and the Santa Ana River are freeway under-crossings (Corps 2019a). Nine such under-crossings of various sizes run beneath SR-91 that can provide connections for wildlife movement to and from the River. The culverts under SR-91 are used by a variety of wildlife. In particular, undercrossing 91-09, known as the “Coal Canyon” underpass, is a highly important wildlife movement corridor for numerous wildlife species, including mountain lions. Additionally, a smaller under crossing 91-17, near the BNSF Railroad Bridge over the Santa Ana River, is an important crossing for wildlife that occurs beneath SR-91 and Green River Road; this culvert is known to be used by bobcats, grey foxes (Urocyon cinereoargenteus), coyotes (Canis latrans), and several other smaller mammalian species.

Natural Communities

The Project area contains an assemblage of natural communities and land uses. Descriptions of the natural community classifications of importance are outlined below (Corps 2019a). See Figures 3 and 4 below.

Cottonwood/Willow/Mulefat Scrub/Woodland/Forest: The Cottonwood/Willow/Mulefat classification occurs in areas that consist predominately of black willow, arroyo willow, Fremont cottonwood, narrow-leaf willow, mulefat, and with minor components of western sycamore (Platanus racemosa).

Mixed Riparian Scrub/Woodland/Forest: The Riparian Mixed classification occurs in areas that consist of roughly 50 percent native riparian vegetation and 50 percent non-native riparian vegetation. Mixed Riparian communities within the Project area include: black willow, Fremont cottonwood, mulefat, elderberry (Sambucus mexicana), cocklebur (Xanthium sp.), caster bean (Ricinus communis), tree tobacco (Nicotiana glauca), and tamarisk (Tamarix sp.).

Coastal Sage Scrub: The Coastal Sage Scrub classification has been applied to areas that consist of 90 percent cover or greater of coastal sage scrub vegetation. The Coastal Sage Scrub areas include California sagebrush (Artemisia californica), California bush sunflower (Encelia californica), California buckwheat (Eriogonum fasciculatum), black sage (Salvia mellifera), and white sage (Salvia apiana).

Mixed Coastal Sage Scrub /Non-Native Grasses/Weeds: The Mixed Coastal Sage Scrub /Non- Native Grasses/Weeds classification has been applied to areas that consist of roughly 50 percent cover of Coastal Sage Scrub and 50 percent cover of non-native grasses and exotics. The Coastal Sage Scrub components includes California sagebrush (Artemisia californica), California bush sunflower (Encelia californica), California buckwheat (Eriogonum fasciculatum), black sage (Salvia mellifera), and white sage (Salvia apiana). Non-native grasses and other exotic plants present include: black mustard (Brassica nigra), poison hemlock (Conium maculatum), starthistle (Centaurea spp.), summer cypress (Kochia scoparia), five-hook bassia (Bassia hyssopifolia), Russian thistle (Salsola tragus), and ripgut brome (Bromus diandrus). Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 56

Non-Native Grasses/Weeds: The Non-native Grasslands and Weeds classification occurs on lands that consist of 90 percent cover or more of non-native grasses and other exotic plants, including: black mustard (Brassica nigra), poison hemlock (Conium maculatum), starthistle (Centaurea spp.), summer cypress (Kochia Scoparia), five-hook bassia (Bassia hyssopifolia), Russian thistle (Salsola tragus), and ripgut brome (Bromus diandrus). These areas are mostly formerly disturbed lands, such as formerly mowed fields or agricultural lands.

Arundo: The Arundo classification has been applied to lands that consist predominantly of the large exotic grass Arundo, with less than 10 percent cover of other vegetation.

Wetlands: The Wetland classification has been applied to areas that are modified to operate as constructed wetlands for water quality treatment.

Open Water: The Open Water classification represents portion of the Project area that consists of surface water bodies, including stream systems, pools, and ponds.

Herbaceous: while not mapped as such by the Corps (see Figure 3 below), at lower elevations in Prado Basin (from about elevations 473 to 485 ft), the Herbaceous cover area consists of a zone of mostly low-height herbaceous plants tolerant of repeated periods and depths of extended inundation (e.g., see McCoy-Sulentic et al. 2017) behind Prado Dam. This zone is visible as a largely treeless area north of Prado Dam in Figure 4 below.

Black Willow Woodland/Forest: while not mapped as such by the Corps (see Figure 3 below), at moderately low elevations in Prado Basin (from about elevation 485-490 ft. to an undetermined upper elevation), the Black Willow cover area occurs surrounding and at higher elevation zone just above the Herbaceous area. This area in the Basin consists of cover highly dominated by large mature black willows (forming gallery forest and some woodland areas), consistent with repeated periods of extended inundation (of shorter durations and depths of inundation than the herbaceous areas in the Basin. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 57

[""°' Agnrulture Cc.ai,tal Sc1ge Scn.,b / Non-Nabve Wee

Figure 3. Natural Communities and Land Uses Upstream and Downstream of Prado Basin (Corps 2019a).

Figure 4. Prado Basin Aerial Image (Google Earth, image acquired February 2018). Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 58

Federally Listed/Candidate Plant Species

Federally-listed and Candidate plant species with considerable potential to occur within the Project area are shown in Table 4 below. The determination on the potential for the species to occur within the Project area is also shown below. Based on existing ecological conditions in the Project area, no Federally-listed or Candidate plant species have a moderate or high potential to occur within the Project area.

Table 4. Federally- and State-Listed and Candidate Plant Species with Potential to Occur in the Project Area22

Potential for Occurrence Plants Federal State in Project Area

Slender-horned spineflower (Dodecahema Endangered Endangered Low leptoceras) Santa Ana River woollystar (Eriastrum Endangered Endangered Low densifolium ssp. sanctorum)

Braunton’s milkvetch Endangered Not listed Low (Astragalus brauntonii)

San Fernando Valley spineflower (Chorizanthe None Endangered Low parryi var. fernandina)

Federally Listed Animal Species

Federally-listed animal species with considerable potential to occur within the Project area are shown in Table 5 below. The Corps’ determination on the potential for these species to occur within the Project area is also shown below. Based on existing ecological conditions in the Project area, several Federally-listed animal species are present or have a moderate or high potential to occur within the Project area. These species and the potential effects from the proposed Project on them, are analyzed in our BO FWS-WRIV-09B0192-20F0606. That analysis is included herein by reference. Designated Critical Habitats for the least Bell’s vireo, southwestern willow flycatcher, California gnatcatcher, and Santa Ana sucker occur within the Project area. Designated Critical Habitat has been proposed for the yellow-billed cuckoo, but does not occur in the Project area (85 FR 11458).

22 Table re-created from the Prado Basin Ecosystem Restoration and Water Conservation Study: Draft Integrated Feasibility Report, Environmental Impact Statement, Environmental Impact Report (Corps 2019a). Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 59

Table 5. Federally- and State-Listed and Candidate Fish and Wildlife Species with Potential to Occur in the Project Area23

Potential for Animals Federal State Occurrence in Project Area Least Bell’s vireo (Vireo bellii Endangered Endangered Present pusillus) Western yellow-billed cuckoo (Coccyzus americanus Threatened Endangered Moderate occidentalis) Southwestern willow flycatcher Endangered Endangered High (Empidonax traillii extimus) Coastal California gnatcatcher Species of Special (Polioptila californica Threatened Present Concern californica) Santa Ana sucker (Catostomus Species of Special Threatened Present santaanae) Concern

Riparian and Aquatic Systems of the Santa Ana River

Along with the Santa Ana River, three major tributaries to the River drain into the Prado Basin; Chino Creek, Cucamonga Creek (which flows into Mill Creek), and Temescal Wash. These tributaries and the River converge upstream of Prado Dam. While a relatively wide riparian area existed in what would become Prado Basin (the area upstream of the head of Santa Ana Canyon) before construction of Prado Dam in the 1940s, the current ecological setting in the Prado Basin is significantly influenced by the presence and operation of Prado Dam. Under current conditions, a combination of locally high groundwater levels, water flows periodically held back within Prado Basin, wastewater treatment plant effluent, and urban runoff contribute to maintain perennial flows into and through Prado Basin, and downstream of Prado Dam on the Santa Ana River. In current conditions, during the winter and spring months, runoff from rain events in the Santa Ana River watershed normally provides substantial natural stream flow in upstream areas; this often results in considerable winter and spring surface flow along Project area reaches several miles upstream and through Prado Basin (the surface flows throughout the mainstem of Santa Ana River were historically naturally perennial, as noted above). During the summer months the surface flows are substantially reduced compared to winter and spring flows, but such flows are typically still present several miles upstream, within, and downstream of the Prado Basin area.

23 Table re-created from the Prado Basin Ecosystem Restoration and Water Conservation Study: Draft Integrated Feasibility Report, Environmental Impact Statement, Environmental Impact Report (Corps 2019a). Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 60

The riparian and aquatic natural communities along the middle portion of the Santa Ana River extend from west of downtown Riverside southwest through the communities of Rubidoux, Pedley, and Norco, and terminate in the vast riparian woodland/forest of the Prado Basin near the near the City of Corona. Though managed primarily for flood risk management, sizable areas of riparian scrub and woodland continue to dot the length of the River, with smaller areas of freshwater marsh, grassland, and coastal sage scrub at the edges of the floodplain. Much of the riparian vegetation upstream of the Prado Basin has been variably overrun with exotic plants over time, diminishing its utility for native wildlife.

The Rancho Jurupa/Rubidoux reach consists of small patches of grassland and riparian thickets along the River. Downstream, the river floodplain widens considerably. West of I-15 into the Prado Basin, the river reaches its widest point, with extensive bottomland riparian woodland and forest areas bordered by some grasslands areas. A large complex of water treatment ponds on the north side of the Prado Basin provide some artificial open water habitats. The Prado Basin is the largest intact patch of riparian woodland/forest in southern California south of the Kern River Preserve.

The Basin supports one of the largest populations of least Bell's vireo, and formerly supported southwestern California’s only known recent breeding sub-population of yellow-billed cuckoo (1-4 pairs in 1986/87; up to 3 pairs in 2001), plus until relatively recently multiple pairs of breeding southwestern willow flycatchers (Layman and Halterman 2012; Audubon 2020). The freshwater marsh habitats in Prado Basin are substantially used by waterfowl and wading birds year round, including winter aggregations of white-faced ibis (Plegadis chihi) (Shuford et al. 1996). Hidden Valley Wildlife Area (about 9 miles upstream of Prado Dam) supports breeding least Bell's vireo, as well as a winter raptor community that reportedly includes ferruginous hawks (Buteo regalis) and prairie falcons (Falco mexicanus) as visitors. Farther east (e.g., Rubidoux), the riparian communities along the River are drier and more constricted, yet still provides habitats for species such as white-tailed kite (Elanus leucurus), yellow-breasted chat (Icteria virens), and blue grosbeak (Passerina caerulea).

Prado Basin consists of a relatively wide mixture of biological resources and natural communities, including; cottonwood/willow riparian forest, riparian scrub, herbaceous riparian, artificial freshwater ponds, freshwater marsh, and riverine zones. Riparian forest is the most dominant wetland natural community type in the Prado Basin. The dominant plant species within the riparian forest of the Project area are black willow, arroyo willow, Freemont cottonwood, California sycamore (Platanus racemosa), and mulefat, with areas of exotic eucalyptus (Eucalyptus sp.).

The riparian areas currently within Project area consist of dynamic natural communities that are naturally both dependent on and adapted to certain levels of episodic flood flows of varying velocities, as well as limited periods of relatively quiescent flood inundation. Short-term levels of winter higher velocity stream flooding flows create natural episodic events of vegetation denudation and sediment scour/transport/deposition that periodically modify swaths of various woody vegetation age classes. This causes the cycling (e.g., the restarting of succession of various seral stages of willow-cottonwood woodland that existed pre-flood flow) of portions of Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 61 these natural communities back to early successional stages. These high stream flow flooding events are highly variable on an annual and decadal basis, creating conditions for a series or mosaic of vegetation age-class areas that range across the channel banks/floodway/floodplain zones in space and time from bare ground and herbaceous natural communities, to older riparian gallery willow forests with little understory. Periodic flood flows of large magnitude and local high velocity (usually in winter) typically denude areas and lay down fresh fluvial deposits that create conditions highly important for some native plant seed germination; for example, Fremont cottonwood is extremely dependent on such flood events for effective reproduction (USDA 2003).

Prado Basin contains expansive riparian areas. At lower elevations in the basin (from about elevations 473 to 485 ft), the cover generally consists of a zone of mostly low-height herbaceous plants adapted to or tolerant of repeated periods and depths of artificially extended inundation, constraints on plant establishment and production, and associated anaerobic stress (e.g., see McCoy-Sulentic et al. 2017). This herbaceous area is surrounded by a zone at higher elevations (roughly above elevations 485 to 490 ft) in the Basin that consists of cover from predominantly large mature or senescent black willows (forming gallery forests in some areas), also consistent with repeated unnatural periods of extended inundation (with shorter durations and shallower depths of inundation than the lower elevation herbaceous areas in the Basin). Variability in space and time of occurrence of both these vegetation zones currently coincides with natural wet or drought periods. At even higher elevations in the Basin, the vegetative cover consists of mostly willow-cottonwood woodland and willow-cottonwood forest with a more natural diversity of dominant and subdominant overstory and understory native woody plant species, stand ages, and under-, mid-, and overstory cover levels.

The riparian areas in the Prado Basin support a diversity and abundance of wildlife species. Sensitive and common neotropical migrant birds, for example, depend on deciduous trees and shrubs in the Basin for foraging during migration and breeding. The mature trees (e.g., black willow) in the Basin provide cavities for some cavity-dependent wildlife, and the taller trees are used by some nesting raptors. The Basin supports a wide variety of native mammal, amphibian, and reptile species. Additionally, the Prado Basin functions as an important wildlife linkage between core ecosystems in the Chino Hills, the Santa Ana Mountains, and the Santa Ana River floodplain.

POTENTIAL EFFECTS OF THE PROPOSED PROJECT ON BIOLOGICAL RESOURCES

The proposed Project includes water conservation and ecosystem enhancement measures within the Prado Basin and along the Santa Ana River both downstream and upstream of Prado Dam. The proposed Project measures would occur within western Riverside County and Orange County. Proposed water conservation would be implemented through the holding of water up to elevation 505 ft. within the Prado Basin, with resultant modified releases from Prado Dam affecting flows downstream in Reach 9 of the Santa Ana River when water conservation measures are implemented. The proposed Ecosystem Restoration Plan measures would be implemented within four different focal areas: SARM Upstream, SARM Downstream, Chino Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 62

Creek, and Mill Creek. The Proposed measures would be implemented beginning in the year 2021, with the ecosystem restoration measures requiring approximately 5 years and with operation and maintenance of some measures occurring for 45 years thereafter through 2071.

Water Conservation Plan

The purpose of the proposed Water Conservation Plan measure is to change the operation of Prado Dam to impound more water and then release the stored water in a controlled manner to optimize recharge of aquifers associated with downstream reaches of the Santa Ana River, including to increase the quantity of water provided to OCWD’s downstream intake structures (Corps 2019a).

In order to improve water conservation for OCWD, an increase to the “water conservation” WSE in Prado Basin is proposed by the Corps during the flood season. As noted above, the proposed Water Conservation Plan component would result in the periodic increase in the holding of water by the Corps within Prado Basin. Specifically, the proposed Plan would increase the allowable WSE in Prado Basin during the flood season (October through February) from 498.0 ft. to 505.0 ft. (NGVD 29) during the 50-year Project period (after year 2023 when the current 5-year deviation expires). This would cause increased time and/or area of inundation in the Basin during periodic water flow events (as compared to the future without project condition after year 2023); this would likely affect sediment deposition and riparian and aquatic habitat types in Prado Basin and along the Santa Ana River.

The proposed Water Conservation Plan would provide up to approximately 10,000 AF of additional temporary storm water capture capacity in Prado Basin for water conservation purposes during the flood season (after year 2023). Based on modeling conducted by the Corps (2019a), the proposed increase in the buffer pool to water elevation 505 ft. would, on average, result in approximately 6,000 AF of additional water per year for conservation and groundwater recharge downstream to OCWD.

Based on the distribution of natural communities in Prado Basin behind Prado Dam, inundation to the higher water levels and/or for longer durations that would occur with the proposed Project would result in the degradation of some riparian habitats (i.e., mainly those occurring within the 490 ft. to 505 ft. elevation contours). These riparian areas currently do provide habitats for considerable numbers of native wildlife species, including some areas that support federally listed species such as the least Bell’s vireo. For example, in 2019, 170 least Bell’s vireo territories occurred below elevation 505 ft. in Prado Basin (Corps 2019a). Based on the current distribution of natural communities in Prado Basin, these affected riparian habitats would likely periodically or generally convert to lower native woody plant understory cover and reduced native plant diversity. This is based on the existing impacts from periodically increased water inundation levels and durations in portions of the Basin.

While the proposal would make the 7.0 ft. increase in the allowable WSE from 498 ft. to 505.0 ft. during the flood season permanent, the effective change in extended inundation periods in Prado Basin would be to shift these average annual periods of extended inundation up about 3 ft. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 63

in elevation in the Basin in the areas below 505 ft., compared to ecological effects of existing dam operations and including past water conservation prior to the temporary allowance for water conservation approved only for years 2018-2023. This is based on modeling24 provided by the Corps (2019a). In other words, the predicted periods of extended artificial water inundation that periodically occur without the proposed Project at, for example, elevation 500 ft., would occur at roughly elevation 503 ft. with the proposed Project Water Conservation Plan; this is based on correlating the modeled days of extended inundation that would occur at particular elevations in the Basin, on average, with and without the Project. As such, the inundation-caused degradation (e.g., periodic reduction in woody plant leaf out, repeated temporary loss of native woody plant understory, reduction in diversity and/or cover of inundation-sensitive native woody plants such as mulefat, etc., as noted above) that currently occurs at elevations 490 to 502 ft. in the Basin without the project would now be shifted up to elevations 493 to 505 ft. in the Basin with the project.25 The approximate surface area of the Prado Basin below the 505 ft. contour is 1,890 acres (Corps 2019a).

It is undetermined if the Project’s proposed monitoring approach for the Water Conservation Plan would be likely to detect such extended inundation impacts effectively. Given the structure of the current proposal, it is unlikely that the Water Conservation Plan mitigation measures for any such Project inundation-caused impacts, should they be detected by the monitoring, would effectively offset such changes. For example, the proposed trigger threshold for initiation of proposed offsetting measures26 is a greater than 30 percent loss of foliage for 2 years with no sign of recovery; this is an artificially high and vague (e.g., is that 30 percent loss in foliage measured in native species only or in all woody plant cover, or are losses in particular native plant species the focus of this metric) trigger threshold. In addition, the proposed offsetting measures are generally planned within the same area as the impacts, likely subjecting any restoration to similar repeated future inundation impacts. This is compounded by the proposed Project reliance on vague concepts of “natural recruitment, non-native removal, active planting…” for offsetting measures. The result in many Project-monitored locations could be, for example, the loss (due to extended inundation effects) of an existing mosaic mix of multi-storied native woody plant species, with the same area ending up heavily dominated by large black willow trees and herbaceous species; yet because this area retains a similar amount of “foliage” it still meets the Project monitoring/offsetting measure criteria.

24 Corps (2019a) DEIS, page 3-46, Table 3-12 includes average days of inundation with and without the Project, at various elevations in Prado Basin. Based on that table: Baseline (500 cfs discharge and seasonal 505) (elevation: inundation days): 498:35, 500:26, 505:2, 510:0 Proposed Project (350 cfs and year-round 505) (elevation: inundation days): 498:86, 500:71, 505:7, 510:2 25 Additionally, see Corps (2019a) DEIS, Tables 12 and 20 (Appendix N). For example, for a modeled 5-year (20 percent recurrence interval) storm event occurring in year 2021: Table 20: (450 cfs release and seasonal 505) (elevation: inundation days): 498:49, 500: 37, 505: 8, 510: 3 Table 12: (350 cfs release and year-round 505) (elevation: inundation days): 498:128, 500:110, 505:20, 510:3 26 “If the habitat monitoring program indicates substantial changes (>30 percent loss of foliage) and prolonged degradation of vegetation between 498 and 505 ft., the affected habitat will be given 2 years to recover on its own (the season of inundation and the following season), prior to active planting. The degraded habitat will be restored within the same area if possible, within two years after the 30 percent degradation trigger is detected. Restoration can either occur through natural recruitment, non-native removal, active planting or some combination.” Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 64

Sediment Management

The stated purpose of the proposed sediment management measure is to offset sedimentation associated with the water conservation plan. This measure is intended to address the additional sediment accumulation that would occur due to the proposed water conservation changes over the 50-year period of analysis, based on analyses performed by Scheevel Engineering (2015). An additional benefit of the proposed sediment removal would be to maintain some water conservation/flood risk management water capacity within Prado Basin that has been lost to the continual sedimentation occurring behind Prado Dam. The proposed Sediment Management Measure direct footprint would be located within Prado Basin and upstream of the Basin on the Santa Ana River (Figure 5 below). The measure would remove a portion of the incoming sediment flowing into the Prado Basin within the Santa Ana River.

Prado Dam acts as a barrier to the natural transport of almost all sediment to the Lower Santa Ana River (below Prado Dam) from the upper river and upstream tributaries. As reported by the Corps, data collection between 1941 and 2008 indicates that at least 25,000 AF of water storage capacity has been lost below the elevation 505 ft. due to sediment accumulation behind Prado Dam, or a loss of about 373 AF per year (Corps 2019a), or about 600,000 yd3 per year. Nevertheless, the greatest deposition in the Prado Basin occurs along the segment of the Santa Ana River between elevations 505 ft. and 524 ft.; the overall sediment load into Prado Basin from the Santa Ana River is estimated as 1,200,000 yd3 per year (Corps 2019a).

Pursuant to the proposed Water Conservation Plan, an additional volume of 10,500 AF of water could be impounded in Prado Basin annually. It was calculated that an additional 3,500 yd3 of silt and clay sediments would deposit annually in Prado Basin from the proposed water conservation changes (Corps 2019a). The estimated increase in sedimentation of 3,500 yd3 would represent a 0.3 percent increase in the overall annual sedimentation volume (Corps 2019a). In each of two proposed sediment management removal events during the life of the project, 125,000 yd3 of sediment would be removed from a reach of the Santa Ana River upstream of Prado Basin, for a total removal of about 250,000 yd3. The excavated sediment would be placed in a sediment storage area over the 50 year life of the Project. The proposed sediment management project would effectively remove the equivalent of about 5,000 yd3 per Project year; this is more sediment than is expected to result from the proposed Water Conservation Plan (3,500 yd3 per year) and would offset the incremental sedimentation increase that would be caused by the proposed water conservation changes. Nevertheless, this 5,000 yd3 per year is 0.4 percent of the annual total sediment input to Prado Basin; this is a small relative amount of sediment removal from the Santa Ana River/Prado Basin. As such, no benefit to Santa Ana sucker or other native fish is likely to accrue from the measure, such as steepened channel slope of the river resulting in a locally increased channel velocities and greater exposure of channel bed gravels for fish spawning. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 65

:ov • -~" • ..... • • ,... • -,,.. • ..,,.. • - • .... Pntdo S.sm E-cosystem Re.storationl Water_ cons~!"•ll!'f' FHSlbllliy S~dy

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Figure 5. Proposed Sediment Management Measure Direct Footprint (in blue).

Ecological Restoration Plan

The stated purpose of the proposed Project’s Ecosystem Restoration Plan measures is to restore the quality and function of aquatic and riparian habitats within the action area of the Project and to address some constraints to regional wildlife movement for both terrestrial and aquatic species (Corps 2019a).

The Project’s proposed Ecosystem Restoration Plan measures would be implemented within the SARM Upstream, SARM Downstream, Chino Creek, and Mill Creek Project focal areas. The measures would be implemented starting in the year 2021, with some activities extending for 50 years. The proposed Ecosystem Restoration Plan measures include elements identified as: Sediment Management, Chino Creek Restoration Improvements, Native Plantings, Invasive Plant Management, In-Stream Habitat Features, and Non-Native Aquatic Species Management (Corps 2019a). Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 66

Chino Creek Restoration Improvements

The purpose of the Chino Creek Channel Restoration Measure is to restore and expand native streambed habitats within the Chino Creek Focal Area. As proposed, existing flows from Chino Creek would be re-routed through a new channel and floodplain to be constructed to the west of the existing creek channel. This new channel is designed to support new areas of unspecified native vegetation communities. Non-native vegetation communities on the site would be removed from the area footprint under the measure during construction, followed by 5 years of herbicide treatment.

As proposed, the creek inflow at the north end of the measure area would be split to provide flows to both the new channel and the existing Chino Creek alignment to support existing aquatic and riparian habitats. Construction would include grading to create a new channel and surrounding perimeter berms to contain flows within the new channel. A portion of the existing Chino Creek channel invert at the northern (upstream) end would be filled in order to force a portion of the split water flow into the new channel. To reduce channel erosion and to help control the hydraulic grade of the new channel, a grouted stone invert stabilizer would be constructed immediately downstream of Pine Avenue, a partially concrete, grouted stone and ungrouted stone drop structure would be constructed in the creek, a pool and riffle structure would be constructed at the outlet of the proposed diversion pipe (utilized to split the creek flow), and a bio-engineered invert stabilizer would be installed at the downstream end of the new channel.

The proposed new Chino Creek channel to be constructed is just south of the El Prado Golf Course, roughly between Pine Avenue to the north and Euclid Avenue to the south. Old remnant channels of Chino Creek run through the site footprint for the new channel; these old channel traces are visible on aerial imagery. Portions of the measure site have been subject to past disturbance, including apparent use of portions of the site over the last 13 years as a borrow pit for fill material for the adjacent golf course.

The design for the new creek alignment to be constructed appears highly engineered by natural stream restoration standards; the design includes channel invert changes, a diversion pipe, relocation of a creek alignment, and multiple channel bed stabilization structures. The proposed design also includes five substantial and apparently “tight” sinuosity curves or meanders for the new section of creek; it is undetermined if the meanders of the proposed new creek channel are consistent with typical designs of relatively stable meanders.27 If the new creek meanders constructed or other features on the site end up being relatively unstable or out of equilibrium, substantial erosion/sedimentation and reconfiguring of the new channel by high creek flows would likely occur during future larger storm events (e.g., see USDA 2007).

27 When natural stream channels are relocated or restored, meander designs are frequently calculated from empirical relationships between channel size or discharge, degree of sinuosity, and meander plan-form descriptors. Restoration projects typically seek a stable but dynamic stream form with natural rates of erosion and deposition. (Langbein and Leopold 1966; Hagerman and Williams 2000; Mecklenburg and Jayakaran 2012) Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 67

The downstream end of the Chino Creek Restoration Improvements measure includes areas around elevation 500 ft, near where Euclid Avenue bridges over Chino Creek. As such, periodic extended inundation up to elevation 505 ft. would recur (as noted above) on small portions of the enhancement site with implementation of water conservation measures in Prado Basin. Any Project enhancement measures directed at establishing and maintaining native riparian woody vegetation at or below 505 ft. on the site are likely to be periodically hampered by repeated extended inundation. That said, most of the site is currently above 510 ft. elevation.

As part of the measure, a total of approximately 3.2 miles of fence would be installed along Pine Avenue and Euclid Avenue, with a primary goal of directing wildlife to existing wildlife corridor crossings. These corridors apparently consist of: 1) a bridge (140 ft-long deck) undercrossing for Chino Creek along Euclid Avenue, and 2) a currently collapsed culvert/bridge on Pine Avenue over Chino Creek, just upstream of the El Prado Golf Course. The subject portion of Pine Avenue road over and on either side of Chino Creek is currently closed and gated-off to vehicle traffic. Just south of the Pine Avenue crossing, Chino Creek as it flows through the El Prado Golf Course is artificially narrowed, rock-lined, and maintained free of most vegetation for about 1,100 ft, with greatly reduced cover for wildlife movement compared to upstream and downstream reaches of the creek. A second primary goal of the proposed fencing is to keep wildlife from attempting at-grade crossings of these roadways. Euclid Avenue, a substantially- trafficked road that crosses Chino Creek within the Project area, reportedly does not have adequate fencing or options for safe wildlife passage, resulting in frequent mortality for wildlife that attempt at-grade crossings (Corps 2019a). Pine Avenue is currently closed to vehicle traffic in proximity of Chino Creek and does not currently present a substantial barrier or risk to wildlife movement; a fence along this closed road section would not likely facilitate wildlife movement or reduce wildlife mortality while the road remains closed. Pine Avenue may be connected to State Route 71 in the future (Corps 2019a); if the closed section of Pine Avenue is re-opened to vehicle traffic, it would likely have the same issues for wildlife movement and mortality as Euclid Avenue unless effective improvements (e.g., an open deck bridge crossing over Chino Creek along with adequate fencing) for north-south wildlife movement along Chino Creek are made. The proposed fencing would be placed on both sides of the noted roadway sections to prevent wildlife entry (and resultant potential mortality from vehicle strikes) from both road sides. The proposed fence alignments would be cleared of vegetation in a zone 30 ft. wide to facilitate fence construction. Once construction is complete, a zone 15 ft. wide along the fence would be kept free of vegetation in the long-term to provide access to the fences and nearby road culverts for maintenance. Along Chino Creek, some of the vegetation to be cleared along the new fences is native riparian woodland.

Construction of this measure would take about 4 months during 2023. The clearing and grubbing phase of the project would start in the fall.

The measure may also include a grouted stone stabilizer to be constructed in Chino Creek within the El Prado Golf Course, just downstream of Pine Avenue. The measure may also include two bio-engineered stabilizers within the bed of Chino Creek (see Figures 6 and 7 below). Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 68

The section of Chino Creek that would be filled includes 2 sections: the upstream-most section would receive partial fill to increase the Chino Creek invert. This creek section would continue to receive creek flow and would remain wetted. The portion of Chino Creek streambed immediately upstream of this increased invert has potential to indirectly aggrade with sediment, due to slowed creek flows caused by the raised channel bed from the proposed new fill downstream.28 It is undetermined if the proposed diversion pipe would be subject to repeated clogging.

As proposed, the downstream section of the creek near the new diversion pipe and downstream of the raised creekbed invert would be completely filled in and no longer receive stream water; this fill would result in a loss of creek open water surface area of approximate 0.40 acres, as well as the loss of surrounding riparian community of undetermined acreage. The riparian/aquatic area of the portion of existing Chino Creek that would remain, but receive greatly reduced surface flows (due to diversion of the majority of creek flows to the new creek section), is roughly 6.9 acres. The aquatic and riparian natural communities in this section are expected to become heavily degraded from substantially reduced ecological functions and values as a result of greatly reduced surface base water flows and eliminated flood flows and fluvial sediment inputs.

The approximate area of new open water surface created by the new cut channel would be 3.24 acres, resulting in a reported net gain of approximately 2.84 acres of open water surface area (aquatic areas) on the site.

After construction the direct footprint of the Chino Creek Chanel Restoration Measure would be planted with undetermined native plants over about 120 acres with the goal of establishing riparian natural communities/habitats. The riparian species to be planted would primarily consist of willow and mulefat; however, the plant species list for all native plantings is currently unspecified. This element would be refined during the Corps’ pre-construction engineering and design (PED) phase.

In sum, implementation of the Chino Creek Channel Restoration Measure would have a direct footprint of about 120 acres. It would cause the removal of about 8.68 acres of willow/cottonwood natural community, 0.07 acres of mixed riparian natural community, and about 1.66 acres of aquatic communities. Reportedly, about 111 acres of the site direct footprint currently consists of exotic vegetation communities (Corps 2019a).

28 In an email of August 6, 2020, the Corps provided pertinent comments to the Service: “Chino Creek flows carry very little sediment and we do not anticipate significant aggradation resulting from this feature. The Corps requests this section be revised to indicate that aggradation is considered unlikely.” (Email from Jesse Ray of the Rock Island District of the Corps to Jon Avery and Carol Roberts of the Carlsbad Fish and Wildlife Office of the Service) Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 69

Figure 6. Proposed Chino Creek Restoration Measure Main Features Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 70

0 Least Bell's Vireo Loc.iton c::t"'''°R""""" r,.1 •- 2019S,oo,n Ex:1an1 or Braicfad ChaMal

Figure 7. Proposed Chino Creek Restoration Measure Details. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 71

Native Plantings:

Chino Creek Focal Area -- The proposed Native Plantings Measure includes activities within the Chino Creek Focal Area, designed to enhance an area in an existing open field to the east of Euclid Avenue and immediately north of Pomona Rincon Road. The 42.9-acre site would be graded to achieve design hydrology for the site and to construct a new maintenance road. The new road would reportedly be needed to provide periodic maintenance for proposed grade control structures to be constructed on the site.

As proposed, the site would be planted with undetermined native riparian species; plantings would include seeding, pole staking, and planting of container plants at undetermined locations across the site. Approximately 42 acres of the site is planned to be converted to riparian forest and scrub communities through the measure. Approximately 30 acres of the site closest to Chino Creek would be converted to riparian forest community. As designed, forested areas passively or actively restored to the site would be dominated by willow species, including black willow nearest the Chino Creek edge, with other willow species including, but not limited to, arroyo willow and red willow further from the creek. As designed, the remaining 12 acres of the 42-acre measure site would be converted to riparian scrub, dominated by mulefat, willows, and other riparian-associated species.

A proposed staging/parking area on the 42.9-acre site would be constructed along with the new maintenance road. While the parking area and maintenance road are not expected to be able to be used by the public (e.g., for recreation), it remains undetermined if this maintenance road and parking area would be used post-construction as a public passive recreation trail and parking lot [as shown in Figure 29 with the Corps 2018 Biological Assessment (Corps 2019a, Appendix G)]. If the maintenance road is used as a recreation trail in the future, the future uses have not been described so potential impacts cannot yet be determined. See Figure 7 above.

Proposed construction and planting activities associated with the Native Planting Measure at Chino Creek would take approximately 3 months. Areas of existing native vegetation on-site that are near the finished design grade for the site would be protected in-place from grading, but the rest of the site would be affected by clearing/grading. As described by the Corps, the site direct footprint consists of 0.4 acres of black willow riparian natural community with the remainder of the site consisting of ruderal pasture. Of the 42.9 acres, the total area of permanent impact from the staging area/parking area and the maintenance road/passive recreation trail would equal approximately 0.73 acres (with 0.55 acres of decomposed granite surface area). The remaining 42.17 acres of the direct disturbance footprint are considered temporary impacts. The clearing and grubbing phase of the measure would start in the in September of 2022, and construction would take approximately 3 months. The site would be planted with unspecified plant species with the goal of native vegetation communities over the 42.17-acre portion of the site.

Maintenance activities on the site would occur annually outside of the bird nesting seasons; it would include trimming and maintaining vegetation along the maintenance road, staging/parking area, and within the 42.17-acre native planting area. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 72

Elevations on the site range from about 493 ft. to 503 ft. currently. As such, periodic extended inundation up to elevation 505 ft. would recur (as noted above per the Water Conservation Plan) on the site with implementation of water conservation measures in Prado Basin. Depending on the final elevations of the finished project, enhancement measures directed at establishing and maintaining native riparian woody vegetation on the site are may be degraded by repeated extended inundation. This extended inundation could cause periodic partial die-off, repeated understory loss, or mortality of much or most of the planted and passively restored native species on the site (such as mule fat). The Corps has indicated that monitoring would be conducted to guide the native plantings to areas above the 505 ft. elevation.

Santa Ana River Focal Area -- The proposed Native Planting measure would include activities within the Upstream SARM Focal Area to develop an enhanced habitats area in an existing open field to the north of the Santa Ana River in Prado Basin and south of the OCWD Wetlands Diversion Channel. This area is visible in Figure 8 below. Most of this area is a set of fields that have been subject to repeated mechanical disturbance, including mowing and use as a borrow pit/stockpile area, at various times over at least the last two decades. Most of the site is currently reportedly dominated by non-native grasses. The site is about 45 acres and is sometimes referred to as the Pheasant Field.

Proposed grading, site prep, invasive species management, planting, and maintenance activities for this site are similar to the Chino Creek Focal Areas Native Plantings measure, except this site does not have a maintenance road/passive recreation trail or a staging area/parking lot. Some additional grading would be required on the site to get the ground surface level closer to the groundwater table. The proposed natural community to be established on the site would be riparian forest dominated by willow. The proposed construction and planting activities would take approximately 3 months starting in Sept 2021. Elevations on site currently range from about 524 ft. to 536 ft. As such, the original and final grade ground surface elevations are/would be substantially above the water elevations subject to extended inundation caused by water conservation in Prado Basin. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 73

Figure 8. Santa Ana River Focal Area Native Planting Area (Corps 2019a).

Mill Creek Focal Area -- The proposed Mill Creek Native Planting Measure includes activities within the Mill Creek Focal Area to develop a riparian forest area in an existing shallow pond basin near Mill Creek. The site is an OCWD non-operational constructed pond (pond E-3 of the OCWD water treatment ponds). The 17.21-acre site would be partially filled to achieve elevations for Project-design hydrology with the goal of supporting riparian forest. About 0.04 acres of the site footprint are currently cottonwood/willow vegetation and 17.17 acres (the remainder of the site) are freshwater marsh; the freshwater marsh natural community would be converted to riparian forest (Corps 2019a). A total of approximately 27,765 yd3 of sediment would be hauled from the Project’s sediment trap (as noted above) to the site using trucks along existing roadways in Prado Basin to fill the site’s existing pond basin. As proposed, perimeter drainage on the site would be maintained by grading a shallow channel around the southern edge of the site. See Figure 9 below.

The site would be planted by seeding, pole staking, and container plants, dominated by willow species, including black willow, arroyo willow, and red willow. Construction and planting activities would take about three months, starting in the fall of 2022. Elevations on the site roughly range from about 513 ft. to 521 ft. As such, the final grade ground surface elevations on the site would be above the water elevations subject to extended inundation caused by water conservation in Prado Basin. Adjacent riparian woodland and forest area occur to the immediate Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 74 north at similar elevations, between the site and Mill Creek, indicating appropriate hydrology on the site for riparian forest can likely be effectively restored. Other potential impacts and benefits of the measure are similar to the Upstream SARM Native Plantings measure.

Figure 9. Proposed Native Plantings, Mill Creek Focal Area (Corps 2019a).

Invasive Plant Management:

The purpose of this measure is to remove invasive plants from the Ecological Restoration Plan focal areas in order to encourage the growth, and increase the biological values, of native vegetation communities on those sites. The invasive plant removal activities would normally start at the upstream extent of the focal areas and progress downstream. After invasive plant removal activity is completed, 5 years of herbicide treatment would occur to reduce the potential for non-native plant communities to be reestablished in the treated areas; small stands of invasive plants intermingled with native plant species would potentially be removed by hand operations, but this is not required as proposed. Large expansive stands of invasive plants in the treatment areas would be removed with heavy equipment and large labor forces. Supplemental plantings, pole cuttings, and seeding of native plants are also associated with this measure. Approximately Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 75

248 acres of extant cover of invasive plants would be removed from the SARM Upstream Focal Area, 14 acres from the SARM Downstream Focal Area, 69 acres from the Chino Creek Focal Area, and 59 acres from the Mill Creek Focal Area.

Invasive species are now widely recognized worldwide as posing threats to biological diversity second only to direct habitat loss and fragmentation (Pimm and Gilpin 1989; Scott and Wilcove 1998). Invasive exotic plants are a major ecological problem in the riparian areas of southern California rivers; this is particularly problematic in areas where considerable direct artificial or natural disturbance has occurred or where the stream hydrology has been modified, but (for some exotic plant species) also occurs in areas where disturbance or modifications are not evident (Dudley 2000). It is rarely possible to eradicate an established exotic plant such as Arundo from a large area in California (e.g., see Bossard et al. 2000). The history of California’s exotic plant eradication projects indicates that there is little likelihood of eradicating an invasive species once it has spread to a substantial acres of a region (e.g., see Hoshovsk and Randall 2000).

As proposed, the initial biomass treatments, plus periodic herbicide follow-up treatments over 50 years, are unlikely to ensure that re-invasion of the focal areas with exotic plants does not occur; re-invasion has occurred repeatedly within similar invasive plant species treatment areas in the southern California riparian areas in the past. While “regular inspections and maintenance, including targeted herbicides treatments would continue…” until Project Year 50, these proposed targeted herbicide treatments appear unlikely to ensure that invasive plant vegetation communities do not substantially reestablish in the Project areas where non-natives were removed. This is of particular concern with exotic plant re-invasions that typically occur following larger flood events and other disturbances. For example, while Arundo is usually associated with rivers that have been physically disturbed and dammed, it also is known to colonize within extant native stands of cottonwoods, willows, and other riparian species, even growing in sites shaded by tree canopy (Dudley 2000). Based on our considerable experience with this issue in the region, the repeated extensive labor, necessary equipment, and material investments involved to control such invasive species are likely to overwhelm the limits of the proposed initial 5 years of herbicide treatments and 45 years of follow-up targeted herbicide treatments from a control perspective. Targeted herbicide treatments alone are quite limited in their abilities to maintain control of several invasive exotic species in the Project area, particularly when these invasive species become intermixed with adjacent native plant species that would be damaged by herbicide foliar spraying. More directed combined mechanical- herbicide treatments (that are more protective of adjacent native vegetation than foliar herbicide spraying), such as repeated “cut-stump” herbicide applications to each new invasive plant invasion on a site, require relatively major commitments to combined hand labor and herbicide application, and sometimes practically entails larger equipment mechanical treatments such as use of mowers for large invasions following expected flood events or equipment disturbance. As proposed, this measure would likely have substantial, albeit temporary benefits to the focal areas.

Cowbird Trapping (Santa Ana River Mainstem Upstream, Mill Creek, and Chino Creek)

The proposed Cowbird Trapping Measure would be combined with existing brown-headed cowbird trapping efforts ongoing in the Project area. It would temporarily increase cowbird trap Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 76

numbers within and surrounding Prado Basin. The proposed cowbird trapping measure would provide an undetermined number of traps (specified as up to 7 traps) within each of the SARM Upstream, Chino Creek, and Mill Creek Project focal areas; the location of traps within the focal areas is undetermined. Proposed cowbird trapping would start in 2021 and would be implemented for 5 years. The Corps has indicated that an unspecified level of cowbird trapping would continue for the 50-year life of the project, but this is otherwise undetermined from the documents provided.29 Depending on the locations and number of traps employed, the proposed cowbird trapping would likely benefit several Neotropical migrant songbird species (including the least Bell’s vireo) in portions of the Project area for about 5 years, or longer if effective cowbird trapping is accomplished in a given area for additional time (including potentially up to 50 years). Cowbird trapping has very limited benefits once terminated, and, as such, we do not anticipate lasting benefits to accrue given the lack of details and potential short-term nature of this element of the Project as proposed.

RECOMMENDATIONS

The FWCA states that “...wildlife conservation shall receive equal consideration and be coordinated with other features of water-resource development projects through the effectual and harmonious planning, development, maintenance, and coordination of wildlife conservation...” (16 U.S.C. 661). As noted above, Section 2 of the FWCA provides direction and authorities to Federal agencies for implementation of measures for both mitigating losses of fish and wildlife resources and for enhancing these resources beyond the scope of offsetting of project effects, including the modification of structures and operations of Federal projects and the acquisition of lands, for fish and wildlife purposes (Smalley and Mueller 2004). The measures outlined below would improve fish and wildlife resources in the Project area; several are larger than the scope of the proposed action. Consistent with the FWCA, below we have identified ways for the Corps, as a member of the Santa Ana River community, to work with the other stakeholders to make the Santa Ana River a more hospitable place for the fish and wildlife resources as outlined herein. The Corps is in a unique place to lead efforts to bring together those stakeholders to work towards a goal of sharing resources, including conservation of the Santa Ana sucker and other sensitive species. Section 2 of FWCA and section 7(a)(1) of the Endangered Species Act both provide general authorities to the Corps for implementation of such measures.

We have eleven main recommendations per the FWCA for the proposed Project:

1. The Corps should work with the other stakeholders (e.g., OCWD, San Bernardino Valley Municipal Water District, Western Municipal Water District, and others) on the Santa

29 In an email of August 6, 2020, the Corps provided pertinent comments to the Service: “While cost-shared cowbird trapping is only scheduled to occur for the initial five year window indicated, OCWD has committed to the continuation of cowbird trapping through year 50. The CAR should be revised to reflect 50-years of cowbird trapping is anticipated to occur…. Cowbird trapping will be implemented in an adaptive fashion with consideration of the broader cowbird trapping needs across the basin, to include consideration of the effectiveness of ongoing cowbird trapping efforts being implemented as part of other projects in the basin.” (Email from Jesse Ray of the Rock Island District of the Corps to Jon Avery and Carol Roberts of the Carlsbad Fish and Wildlife Office of the Service). Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 77

Ana River to develop and publish a water budget report for the Santa Ana River to enumerate and map all appreciable natural and artificial water inputs and outputs on the River, including known groundwater pumping, water diversions, wastewater releases, and within-River transfers. The Corps should work to facilitate a better understanding of the groundwater basins and known groundwater levels (e.g., from well monitoring) along the River from Seven Oaks Dam to below Prado Basin. This information would assist in identifying areas with current and likely historical groundwater-surface water interactions within the River and where groundwater diversions could be impacting surface flows along the River. With this information, the Corps and the other stakeholders on the Santa Ana River could approach water management more holistically.

2. The Corps should move away from project-by-project conservation (offsetting) measures on the Santa Ana River and utilize the water budget and groundwater information identified above to work with the other stakeholders in developing target hydrographs and key groundwater levels along the River based on the requirements of target listed/sensitive species and natural communities. For example, we suggest that target hydrographs be developed that would functionally support viable habitats for populations of Santa Ana sucker, arroyo chub, southwestern willow flycatcher, and least Bell’s vireo along appropriate reaches of the River. These should be compared with and differentiated from hydrographs that would support southern California steelhead and yellow-billed cuckoo.

3. Based on the information developed in #2 above, the Corps and its partners should determine functional flow criteria then estimate the necessary environmental flows that, if implemented, would likely accomplish the target species hydrograph and groundwater metrics. These estimated environmental flows should be published in a report to be provided to all the stakeholders on the River, including the Service.

4. With the estimated environmental flow needs from #3 above, the Corps should lead the coordination and partnering with all the stakeholders (i.e., local water districts, wastewater agencies, watershed authorities, sand and gravel mining companies, and flood risk management agencies) to map out the necessary modifications to releases, withdrawals, and discharges throughout the River system to establish these environmental flows, and in so doing maintain essential groundwater levels in dry, average, and wet conditions on the River on an ongoing basis. These environmental flows would provide for more holistic management of the Santa Ana River, including a possible return to a more natural state that would more sustainably support Santa Ana sucker and other native fish and enhance or re-establish other sensitive species’ habitats (e.g., southwestern willow flycatcher and least Bell’s vireo) in some currently degraded areas of the River. We expect that such flows would require some transfers of water among the stakeholders, but this can be accomplished with minimal losses (e.g., from evapotranspiration or flows to the ocean). We encourage the Corps and OCWD to apply Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 78

for California Proposition 1 funds30 for projects that would result in enhanced stream flows for fish, wildlife and other beneficial uses on the Santa Ana River.

5. The Corps should work with the other stakeholders and the Service on an analysis of effects to Santa Ana sucker and Santa Ana sucker Critical Habitat along the Santa Ana River from the combined operations of Seven Oaks Dam, Prado Dam, and other facilities along the River that affect sediment transport and thus the availability of habitat for the sucker. The Corps should work with its partners to develop a hydrology/sediment transport management plan for maintaining and re-establishing habitats for the species (consistent with a Priority 1 action in the sucker Recovery Plan (USFWS 2017)) and other extant and extirpated fish native to the Santa Ana River.

6. The Corps should evaluate and report to the Service on the pertinent water quality characteristics of releases and flows below Prado Dam to determine potential impacts of poor water quality on native aquatic resources, including the Santa Ana sucker and other native fish. The causes of any problematic water quality (notably, high turbidity levels and effects on native fish) in stormflows or base flows below Prado Dam should be determined and reported to the Service. The Corps should develop remedies for any ecological water quality problems in such flows that are likely associated with Corps activities and/or facilities, such as water impoundment within Prado Basin or dam operations/structures. Conservation Measure 14 above would likely partially address this recommendation.

7. The Corps should work with its partners to identify opportunities to implement a spawning gravel supplementation program on the Santa Ana River. Rounded gravel appropriate for native fish spawning should be periodically added to Santa Ana sucker potential habitat in the River in and above selected reaches where otherwise appropriate conditions for the sucker exist and where these conditions will likely be restored, such as with the environmental flows outlined above. This supplemental rounded gravel would partially offset impacts of the currently modified fluvial characteristics of the River and assist in maintaining functional breeding conditions for the Santa Ana sucker and other native fish. This measure would be quite similar to the several Corps gravel augmentation projects in the western U.S., such as the Corps’ Lower Yuba River Gravel Augmentation Project (Corps 2013) and the Corps’ Gravel Augmentation on the Trinity River Project (Corps 2017); these were designed to enhance fish habitat below Corps dams.

8. The Corps and OCWD should further partner with the Santa Ana Watershed Project Authority and other local agencies and organizations to more effectively control invasive animal and plant species in the long-term along the entire Santa Ana River mainstem and its tributaries, as compared to the project-by-project, regional, and mitigation bank

30 The Water Quality, Supply, and Infrastructure Improvement Act of 2014 (Proposition 1) authorized the California State Legislature to appropriate $200 million to the California Wildlife Conservation Board (WCB) to fund projects that result in enhanced stream flows (i.e., a change in the amount, timing, and/or quality of water flowing down a stream, or a portion of a stream, to benefit fish and wildlife). WCB distributes these funds on a competitive basis through the Stream Flow Enhancement Program. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 79

measures currently employed or required. Pursuant to the proposed Invasive Plant Management elements of the proposed Project, the Corps and OCWD should modify the Project, or use resources available to them beyond the Project, to include substantial commitments to a combination of repeated mechanical and chemical control (e.g., cut- stump or similar treatments), as necessary, to maintain the Project focal sites predominantly free of important invasive species (e.g., less than 1 percent cover of invasive species such as Arundo) for the 50-year Project term. In addition, the Corps and OCWD should similarly periodically (e.g., every five years) control invasive plant species on the properties these agencies control and where they perform mechanical equipment work (such as levee, channel, and road maintenance edges) in the Project area, so as prevent the propagation of these species on these sites and into adjacent areas, in the long-term. The Corps and OCWD should provide recurrent reporting of these activities to the Service that includes actual locations and extents of treatment actions and documentation of the success in controlling invasive plants.

9. The Corps should work with OCWD and its other partners to specify and provide a coordinated effective cowbird trapping program across the entire Project area in the long- term that fills gaps where appropriate and complements the spatial and temporal limits of other trapping efforts in the area.

10. The Corps and OCWD should continue to seek opportunities with the El Prado Golf Course into the future, as their management needs may change over time, in order to restore a functional riparian zone vegetated with native woody species (e.g., 50 ft. on both sides of creek) and with buffers along Chino Creek through the golf course. This would provide for reduction of ecological impacts from surrounding land uses including landscaping, enhancement of some aquatic and riparian ecosystem functions on site, and improvements to north-south wildlife movement along Chino Creek through the golf course area. This would be consistent with the fencing and ecological enhancement goals proposed in the Project’s adjacent Chino Creek Restoration Measure.

11. The Corps should work with the Service and its applicants early in the project planning process to develop conceptual restoration plans and conservation measures that provide more specific details on the basic hydrological characteristics, general minimum enhancement/active restoration features, expected passive restoration changes, specific planting lists/palettes (as compared to generally specifying “native plantings”), etc., for its proposed projects that are intended to support the ecological enhancement or restoration objectives. Additionally, the Corps should work with its applicants to provide clear minimum basic specifics of what would be accomplished within proposed conservation measures (for example, specifying “ a minimum of 5 cowbird traps would deployed…”, as compared to specifying a maximum of “up to 5-7 traps”). These suggestions will allow for the Service and other agencies to perform basic analysis and evaluate the potential for minimum success and the anticipated resultant functions of the measure for incorporation into future restoration planning undertaken by those entities. Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 80

If you have any questions you have regarding this letter, please contact Jon Avery, Federal Projects Coordinator, at 760-431-9440, extension 309.

Sincerely,

for Scott A. Sobiech Field Supervisor Colonel Julie A. Balten (FWS-OR-19B0097-20CPA0162-20E02870) 81

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Zeedyk, B. and V. Clothier. 2015. Let the Water Do the Work: Induced Meandering, an Evolving Method for Restoring Incised Channels. Quivira Coalition. Prado Basin Feasibility Study Coordination Act Report Response to USFWS Recommendations Corps’ Response to Recommendations 1-4 Releases from Prado Dam are shaped based on a variety of factors, which include flood risk, potential damages to downstream infrastructure, ecosystem needs, and regional water conservation needs. The Corps works to balance competing needs within the system, including ecological resources, and the success of least Bell’s vireo in the basin highlights that ongoing operations of Prado Dam do provide ecological benefits. However, many of the other factors identified in recommendations 1-4 the Corps has little or no ability or authority to control, such as groundwater withdrawals, wastewater releases, sand and gravel mining, water diversions, and water transfers. These Recommendations far exceed the scope, scale and authority of this project, or any existing project the Corps currently has on the Santa Ana River. Recommendations 1-4 discuss managing the Santa River on a watershed scale and include consideration of numerous management activities outside of the scope of this study. On page 48, the CAR discusses the Corps and TNC partnership under the Sustainable Rivers Project (SRP). However, the SRP does not provide a mechanism through which the Corps can control or direct other activities in the watershed, as referenced in the paragraph above. Rather, the SRP provides a framework for evaluating dam operations in an ecological context and determining if operations can be modified for ecological benefits, given existing constraints.

Corps’ Response to Recommendation 5 Development of a hydrology/sediment transport management plan for maintaining habitat for the Santa Ana sucker is beyond the scope of the current study. The Corps does not own or operate Seven Oaks Dam and evaluating the operation of Seven Oaks Dam is outside of the authority and scope for this study. Within the current study authority and scope, the Corps evaluated options to provide sediment transport around Prado Dam and address sediment transport in the project area. The Corps developed a focused sediment management feature for the purposes of ecosystem restoration that we anticipated would provide significant benefits to both Santa Ana sucker and associated habitat. This feature is included in two of the action alternatives. However, the Service had substantial concerns regarding potential impacts associated with sediment management, and subsequently this feature was removed from the recommended plan. The Service has provided the Corps with comments and suggestions in the past regarding sediment transport, which the Corps reviewed, considered, and responded to. However, as previously communicated to the Service and as described in the IFR, the options the Service expressed interest in proved to be infeasible and impracticable within the context of Prado Dam operations or within the context of this study. More broadly, the Corps has developed the required NEPA and ESA documents and consulted on Prado Dam actions, when appropriate, regarding potential effects to Santa Ana sucker and its designated critical habitat. These documents contain cumulative impact analyses pursuant to the requirements of NEPA and the ESA. The Corps will continue to analyze cumulative impacts within the context of NEPA and the ESA, if new federal actions trigger the need for additional evaluation. Corps’ Response to Recommendation 6 In coordination with USFWS during the ESA consultation process for the change in the water conservation plan, OCWD committed to an evaluation of water quality above and below Prado Dam (Conservation Measure 14). The Corps anticipates that the data resulting from implementation of Conservation Measure 14 will partially address this recommendation.

Corps’ Response to Recommendation 7 Within the context of this ecosystem restoration study, gravel supplementation was not considered a feasible measure. Corps policy regarding ecosystem restoration projects provides guidance that studies should pursue alternatives that would result in a self-regulating system (ER 1165-2-501), and WRDA 2016 (Section 1161) generally limits the operation and maintenance of non-structural features in ecosystem restoration projects to ten years. The importation of supplemental gravel would require continued future maintenance in perpetuity in order to maintain any substantive benefits if concurrent changes to hydrology and geomorphology did not also occur. Such long-term maintenance is not supported by Corps planning policy and is limited pursuant to WRDA 2016. Without long-term maintenance, gravel importation would not sustain long-term benefits. As a result, the Corps and OCWD did not formulate for gravel supplementation and cannot commit to the long-term importation of gravel within the scope of this study, as recommended. As discussed in response to recommendation 5 above, the Corps and OCWD developed a sediment management measure as part of this feasibility study and included it in two action alternatives, but this measure is not part of the recommended plan.

Corps’ Response to Recommendation 8 As discussed in response to recommendation 7 above, the Corps’ ecosystem restoration program is directed to seek self-regulating systems and WRDA 2016 provides limitations on long-term maintenance programs for non-structural features within an ecosystem restoration project. The overarching purpose of the Corps’ ecosystem restoration program is to restore aquatic habitats where solutions primarily involve modifying the hydrology or geomorphology of the system, and a comprehensive control of invasive animal and plant species on a watershed scale does not align well with this mission. OCWD has committed to continuing to implement maintenance of non-native vegetation and cowbirds beyond the 10-year maintenance window for non-structural features. OCWD has committed to continuing maintenance through the life of the project at the same level of effort of the initial maintenance, provided that the feasibility of such maintenance is not negatively impacted by factors beyond OCWD’s control. Such factors include, but are not limited to, regulatory changes or legal risks that restrict herbicide use, major fire, major flood, or new non- native pests that affect riparian vegetation. Within the context of this study, the Corps’ study authority, and the Corps’ broader restoration program, the invasive vegetation management plan and cowbird trapping measure, supplemented with OCWD’s long-term commitments, have addressed invasive animals and plants to the maximum extent feasible.

Corps’ Response to Recommendation 9 While cost-shared trapping would only continue for five years, OCWD has committed to maintaining cowbird trapping for the life of the project. Cowbird trapping will be implemented in an adaptive fashion with consideration of the broader cowbird trapping needs across the basin, to include consideration of the effectiveness of ongoing cowbird trapping efforts being implemented as part of other projects in the basin.

Corps’ Response to Recommendation 10 The Corps and OCWD coordinated with golf course staff during the feasibility study. However, we were not successful in developing restoration measures on the golf course that would be amenable to the course, given their management needs and concerns. Since no feasible measures were identified that would not significantly impact the existing golf course operations and ongoing recreation, restoration measures on the golf course were not pursued further in the course of this study. However, the Corps remains open to future restoration opportunities on the golf course, should the opportunity, including authority and funding, for such a project arise.

Corps’ Response to Recommendation 11 The Corps provided conceptual restoration plans for all measures included in this study at a level of detail commensurate with Corps’ planning policy. Under current Corps’ planning policy, a greater of level of detail for conceptual restoration plans is not developed during feasibility, but rather during the pre-construction engineering and design phase (PED), which occurs after the Chief’s Report has been signed. However, the Corps and OCWD have committed to continued coordination with the Service during PED for this project, if the project is funded for design, and authorized and funded for construction. The feasibility report discussed and evaluated a range of restoration features, both minimum enhancements and much larger restoration features. This study provided an evaluation of expected ecological benefits in the form of a habitat evaluation model, which documented the expected benefits resulting from each measure evaluated. In addition, this study included a written narrative of expected benefits in addition to the outcome of the habitat evaluation models. The study included a list of restoration objectives, as well as a monitoring and adaptive management plan, which documents how success of restoration measures will be evaluated and documented. These documents were included in the package for other agencies to review and provide input on during the NEPA public review period. For this study, the adaptive management plan was revised in coordination with USFWS staff following comments received during the public review period, as well as in coordination with the formal consultation as part of the Corps’ Endangered Species Act compliance. During the next phases of the project, USFWS has been included as a member of the adaptive management team. As a member of the AMT, USFWS is shall be invited to review monitoring results and provide advice on recommended adaptive management responses.