00-31-24-01_1-5-A_2023_05_31_2022-0014986-S7-I_SD_USMCA_Transboundary_Flows_FWS.pdf

In Reply Refer to:

2022-0014986-S7-I_SD

May 31, 2023

Sent Electronically Lily Lee Manager, Infrastructure Section Water Division U.S. Environmental Protection Agency Region 9 75 Hawthorne Street San Francisco, California 94105-3901

Gilbert Anaya Chief Environmental Management Division U.S. International Boundary and Water Commission United States and Mexico United States Section

Subject: Informal Section 7 Consultation for the United States-Mexico-Canada Agreement

(USMCA) Mitigation of Contaminated Transboundary Flows Project (Alternative 1) Project, San Diego County, California

Dear Lily Lee and Gilbert Anaya:

This is in response to the U.S. Environmental Protection Agency’s (EPA) and U.S. International Boundary and Water Commission’s (USIBWC) request for our concurrence that the United States- Mexico-Canada Agreement (USMCA) Mitigation of Contaminated Transboundary Flows Project (Alternative 1) is not likely to adversely affect the federally endangered least Bell’s vireo (Vireo bellii pusillus, vireo) and its designated critical habitat, light-footed Ridgway’s (=clapper) rail [Rallus obsoletus (=longirostris) levipes; Ridgway’s rail], San Diego fairy shrimp (Branchinecta sandiegonensis), Quino checkerspot butterfly (Euphydryas editha quino; Quino), salt marsh bird’s beak (Chloropyron maritimum subsp. maritimum), San Diego ambrosia (Ambrosia pumila), thread-leaved brodiaea (Brodiaea filifolia), Orcutt’s spineflower (Chorizanthe orcuttiana), San Diego button celery (Eryngium aristulatum var. parishii), willowy monardella (Monardella viminea), California Orcutt grass (Orcuttia californica), San Diego mesa mint (Pogogyne abramsii), and Otay mesa mint (Pogogyne nudiuscula); and the federally threatened coastal California gnatcatcher (Polioptila californica californica, gnatcatcher), San Diego thorn-mint (Acanthomintha ilicifolia), Otay tarplant (Deinandra conjugens), and spreading navarretia (Navarretia fossalis), in accordance with section 7(a)(2) of the Endangered Species Act of 1973 (Act), as amended (16 U.S.C. 1531 et seq.).

The project is located at the U.S.-Mexico border in the Tijuana River Valley in San Diego, Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 2

California. We received EPA’s letter requesting our concurrence on May 25, 2022, and a subsequent letter clarifying that EPA and USIBWC are joint federal lead agencies for the consultation on May 10, 2023.

This consultation is based on the following information: 1) your May 25, 2022 and May 10, 2023 letters, 2) the Draft Biological Assessment for the USMCA Mitigation of Contaminated Transboundary Flows Project (BA, Stillwater Sciences 2022), 3) the project’s Programmatic Environmental Impact Statement (PEIS, EPA and USIBWC 2022), 4) the Update of Rempel Water Balance for the USMCA Mitigation of Contaminated Transboundary Flows Project (Rempel Update, ERG and PG Environmental 2023); 5) the Supplemental Information Regarding Potential Nutrient and Salinity Impacts to California Cordgrass and the Light-footed Ridgway’s Rail (EPA and USIBWC 2023); 6) emails and meetings with EPA, USIBWC, and their biological consultants.

CONSULTATION HISTORY

We received your letter requesting initiation of informal consultation along with the draft BA (Stillwater Sciences 2022), on May 25, 2022. Following initiation of consultation, we coordinated with EPA, USIBWC, and the project’s consultants during several meetings, a site visit, and emails to evaluate the project’s estimated reductions to existing freshwater input in the Tijuana River Valley.

This included reviewing historical transboundary flows and natural stream flow data, evaluating historical vegetation and hydrology conditions, and coordinating with regional and biological experts. We also coordinated with EPA and USIBWC regarding the project’s proposed conservation measures and direct impacts to vegetation. On January 20, 2023, we became aware that we had previously completed consultation in 1994 (1-6-94-F-13) with EPA on a previous phase of the project to construct the South Bay International Wastewater Treatment Plant (ITP) for primary treatment of up to 25 million gallons per day (MGD) of untreated wastewater from Mexico.

Following this discovery, we worked with EPA and USIBWC to gather information collected during and following the previous consultation to determine how it relates to the proposed project and help inform potential impacts. On April 12, 2023, we received the Rempel Update, which updates a hydrogeological assessment prepared in support of the ITP’s original construction (Rempel 1992) and evaluates the project’s potential to change groundwater levels in the Tijuana River Valley (ERG and PG Environmental 2023). On April 19, 2023, we received the Saltmarsh Impacts Update, which evaluates the project’s potential to alter saltmarsh habitat downstream of the project site. On May 10, 2023, we received a letter from EPA noting that USIBWC is a joint federal lead agency for this consultation, requesting our concurrence that the project is not likely to adversely affect salt marsh bird’s beak, and proposing additional conservation measures to address impacts to listed species. We provided a draft Project Description to EPA and USIBWC on May 17, 2023. We received comments from EPA on May 25, 2023, which have been incorporated into this consultation. The complete project file addressing this consultation is maintained at the Carlsbad Fish and Wildlife Office

(CFWO).

PROJECT DESCRIPTION

The EPA and USIBWC, as joint federal lead agencies, are proposing to fund and implement the project to reduce transboundary flows from Tijuana that convey pollutants, sewage, and trash into the U.S. and cause adverse public health and environmental impacts in the Tijuana River watershed and adjacent coastal areas. We previously completed formal section 7 consultation with the EPA for

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 3 construction of the South Bay Land Outfall (SBLO), which is a tunnel extending from the from the ITP and the City of San Diego’s South Bay Water Reclamation Plant (SBWRP) to a point near the coastline on April 16, 1990 (1-6-90-F-17). We completed an additional consultation on the initial construction and operation of the ITP on April 19, 1994 (1-6-94-F-13). Our 1994 biological opinion addressed the potential impacts from the first phase of construction and operation of the ITP to treat 25 MGD of dry-weather wastewater from the International Collector, a 1.5-mile pipe that carries untreated wastewater from downtown Tijuana, Mexico and diverted flows from the Tijuana River. It also addressed construction of the canyon collector system that captures and conveys untreated wastewater from Goat Canyon and Smuggler’s Gulch to the ITP, and construction of the South Bay Ocean Outfall (SBOO), which is a pipeline that conveys treated wastewater from the SBLO 3.5 miles offshore.

Facilities in Mexico that currently divert and treat wastewater and dry-weather flows are a complex network of pipes, pumps, and treatment plants. La Morita Wastewater Treatment Plant (WWTP) and Arturo Herrera WWTP are in east Tijuana and discharge treated effluent into the Tijuana River upstream of the border. The Planta de Bombeo Comisión International de Limites y Aguas pump station (PB-CILA) is a river diversion system located along Tijuana River just south of the border (Figure 1). When PB-CILA is functioning properly, all dry-weather flow (up to 23 MGD) in the Tijuana River is diverted before transboundary flows (dry-weather flows that cross the international border) occur. The diverted flow is routed to Pump Station 1A (PB1-A) or into the International Collector. When operating properly, PB1-A receives diverted river water from PB-CILA and conveys these flows to an outfall into San Antonio de los Buenos (SAB) Creek. PB1-A’s current capacity is about 11.5 MGD and is considered the limiting factor that prevents more flow from the being diverted from the Tijuana River. When PB1-A is malfunctioning, PB-CILA either pumps diverted river water into the International Collector or shuts off and allows transboundary flows to occur in the Tijuana River. The International Collector receives untreated wastewater from downtown Tijuana and the portion of diverted river water from PB-CILA that is not sent to PB1-A.

At the west end of the International Collector, a diversion box directs about 25 MGD to the ITP with the remainder being pumped to PB1-B. PB1-B receives flows from the International Collector and sends them to the San Antonio de los Buenos Wastewater Treatment Plant (SABTP), which discharges into the ocean via SAB Creek. When PB1-B is operating at reduced capacity, the ITP must accept a higher proportion of the flows in the International Collector, even if this results in exceeding the ITP’s design capacity. Three canyon pump stations in Matadero Canyon (the portion of Smuggler’s Gulch in Mexico) and Los Laureles Canyon (the portion of Goat Canyon in Mexico), pump wastewater from the sanitary sewer to the SABTP. The canyon pump stations do not convey any “disconnected” flows that drain directly into the canyons.

Deficiencies in the treatment, piping, and pump station network in Tijuana contribute to contaminated transboundary flows entering the U.S. via coastal waters of the oceans, the Tijuana River, and tributaries that flow north through canyons to the Tijuana River Valley and Estuary (Figure 2). As a result of design and capacity limitations, Tijuana River water and untreated wastewater are pumped from PB1-A and PB1-B either directly to SAB Creek or to SABTP for inadequate treatment before discharge to the ocean, resulting in about 28.2 MGD of untreated wastewater being discharged into the ocean and carried north along the coast into the U.S.

Breakdowns and power outages at PB-CILA and the canyon pump stations, or physical blocking of the diversions inlets by trash, frequently result in dry-weather flows crossing the border. PB-CILA was upgraded in 2021 to provide a capability to divert up to 35 MGD; however, this upgrade will not

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 4 prevent dry-weather river flows unless supplemented by further infrastructure improvements.

Deteriorating infrastructure in Mexico also contributes about 10 MGD of untreated wastewater into the Tijuana River. Mechanical issues at the ITP can also occasionally contribute to transboundary flows when inflow is restricted and backed up into Mexico.

Dry-weather flows in the Tijuana River south of the border typically range between 20 to 30 MGD, including about 14 to 15 MGD of treated effluent from the WWTPs and flows from the Alamar River. The remaining 6 to 16 MGD consists of untreated wastewater and urban runoff.

EPA and USIBWC have identified two alternatives to address the purpose and need of the project in the PEIS: a limited funding approach with four Core Projects (Alternative 1), and a more comprehensive solution that would require additional funding and include the four Core Projects and Supplemental Projects (Alternative 2). Because implementation of the Supplemental Projects would require additional funding that has not yet been identified, EPA and USIBWC have requested consultation for implementation of the four Core Projects in Alternative 1 (EPA and USIBWC 2022).

Core Projects (Alternative 1)

Some components of Alternative 1 will take place in Mexico and will only move forward with support and funding contributions from appropriate Mexican authorities. Components of Alternative 1 that will take place in Mexico are not considered in this consultation unless transboundary flows will be affected.

Project A: Expanded International Treatment Plant (ITP)

Project A involves expanding wastewater treatment capacity at the ITP from 25 MGD ITP to up to 60 MGD (Figure 3). The primary purpose of this expansion is to reduce impacts to the U.S. coast by treating wastewater from the International Collector in Mexico that otherwise would be discharged to the Pacific Ocean via SAB Creek with inadequate or no treatment. The expansion may also provide treatment for sewage collected in the canyons (Project B), and treat additional sewage flows produced by the future population of Tijuana as it continues to grow. Treated wastewater would continue to be discharged to the ocean through the SBOO. Site modifications of the existing ITP facility would be needed to expand the treatment capacity, including filling in a portion of the site, relocating a portion of Dairy Mart Road that crosses through the ITP, and enclosing or relocating a stormwater swale. Up to 40,000 cubic yards of fill material will be sourced from existing sediment capture and extraction sites within the Tijuana River Valley, such as the existing sediment basins in Goat Canyon or Smuggler’s Gulch. A temporary staging area may be needed in the undeveloped 25-acre southwest quadrant of the ITP parcel and in portions of the 4-acre parcel northwest of the ITP.

Project A is estimated to be completed no later than 2027.

Project B: Tijuana Canyon Flows to ITP

Project B involves the installation of a wastewater conveyance system from Matadero Canyon and Los Laureles Canyon in Mexico to the expanded ITP for treatment. The three Mexican pump stations in the canyons in Mexico will remain in place as backup to pump flows from the canyons to SABTP or SAB in the unlikely case of failure of a Project B pipeline in the U.S. The purpose of Project B is to reduce the amount of dry-weather wastewater flows that are currently discharged with little to no

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 5 treatment to the ocean via the SAB Creek. The volume and frequency of dry-weather transboundary flows in Goat Canyon and Smuggler’s Gulch may also be reduced by eliminating the reliance on pump stations whose mechanical issues may cause occasional wastewater overflows into the canyons in Mexico. Four pipelines (Reaches 1-4) will be installed in the canyons in Mexico to convey wastewater across the border to the conveyance line in the U.S. (Reach 5). Reach 5 will be trenched through existing roadways in Smuggler’s Gulch and along Monument Road to the ITP (Project B1 in the PEIS). Directional drilling will be used to connect the sections between Mexico and Reach 5 beneath the border for about 1,000 feet (Figure 4).

The current wastewater flow from the canyons is 6.3 MGD, and the new conveyance system will collect up to 12.7 MGD for treatment at the ITP and discharge at the SBOO to accommodate future population growth and flow increases over time. Construction of Project B, including the components in Mexico, will take about 2 years to complete. An estimated construction start date is not yet known.

Project C: Tijuana Sewer Repairs

Project C includes rehabilitating or replacing targeted sewer collectors in the Tijuana metropolitan area in order to reduce the amount of untreated wastewater that currently leaks from the sanitary sewer system and enters the Tijuana River. This project will reduce Tijuana River flow volumes by an estimated 5 MGD, which will result in less frequent transboundary flows caused by river flow rates that exceed the PB-CILA diversion capacity and help ensure that more wastewater in the sewer system is successfully conveyed to the ITP for treatment. Construction of Project C will take about 3 years to complete for each individual component. An estimated construction start date is not yet known.

Project D: APTP Phase 1

Project D includes construction and operation of a 35-MGD Advanced Primary Treatment Plant (APTP) for advanced primary treatment of diverted water from the existing PB-CILA diversion in Mexico, rehabilitation and extension of the existing force main from PB-CILA to the new APTP, installation of other new supporting facilities, and associated site modifications. The main purpose of this project is to reduce impacts to the U.S. coast by treating diverted river water that otherwise would be discharged to the ocean via SAB Creek with inadequate or no treatment. This project will also reduce the frequency of transboundary river flows by eliminating the use of PB1-A, whose mechanical issues indirectly cause occasional shutdowns of the PB-CILA diversion. The APTP will operate independently of the ITP and will discharge treated effluent to the ocean through the SBOO.

The PB-CILA diversion in Mexico currently conveys diverted river water to PB1-A through a 42-inch force main. Project D will extend this line to direct flows from PB-CILA to the APTP, thus bypassing PB1-A and allowing it to be decommissioned. Bypass of PB1-A will allow PB-CILA to operate whenever the river flow rate is 35 MGD or less to divert river flows to the APTP. Open trenching will occur within the ITP site and along Tia Juana Street to install the force main line from the border to the APTP.

The APTP site will be constructed in the north area of the ITP parcel, immediately north of the ITP secondary treatment units and south of Tia Juana Street (Figure 5). Staging will likely occur on the undeveloped 25-acre southwest quadrant of the ITP parcel. The APTP will be designed and

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 6 constructed to allow for potential expansion under Phase 2. Reinitiation of section 7 consultation would be needed if EPA and USIBWC proceed with expansion of the APTP in Phase 2.

Direct Vegetation Impacts and Conservation

The proposed project will result in direct impacts to mostly non-native and disturbed habitats within the U.S. during construction of Projects A, B, and D (Table 1). Native habitats that will be impacted occur mainly in the existing ITP parcel (Projects A and D) and within the trenching area associated with Project B. The project will also implement an invasives removal plan within about 27.5 acres of IBWC property within the Tijuana River Valley and fund restoration of13.5 acres of the County of San Diego’s Tijuana River Valley Invasive Species Removal and Restoration Project (ISRRP, HELIX 2023). The project will also remove/restore 26 acres of Tamarisk-dominated areas from Tijuana Estuary.

Table 1. Project impacts to vegetation communities

Vegetation Community Temporary Impacts (acres)

Permanent Impacts (acres)

Total Impacts (acres)

Project A (Expand ITP) and Project D (APTP Phase 1)

Mulefat scrub 0.2 1.2 1.4

Broom baccharis scrub 0.1 0 0.1

Saltbush scrub 0.1 0 0.1

Non-native grassland 5.5 5.5 11

Disturbed/non-native 1.1 8.5 9.6

Project B (Tijuana Canyon Flows to ITP)

Coastal sage scrub 0.15 0 0.15

Lemonade berry scrub 0.05 0 0.05

Grand Total 7.2 15.2 22.4

Conservation Measures

EPA and USIBWC will implement the following conservation measures to avoid and minimize impacts to the listed species and critical habitat addressed in this consultation. We consider these measures to be part of the proposed action, and our analysis assumes they will be implemented.

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 7

General Measures

CM 1. A CFWO-approved biologist (Biological Monitor)1 will be on site: (a) during clearing and grubbing; and (b) weekly during project construction within 500 feet of gnatcatcher or vireo habitat to ensure compliance with all conservation measures. EPA/USIBWC will submit the biologist’s name, address, telephone number, and work schedule on the project to the CFWO at least 5 working days prior to initiating project impacts. The contract of the Biological Monitor will allow direct communication with the CFWO at any time regarding the proposed project. The Biological Monitor will be provided with a copy of this consultation. The Biological Monitor will be available during pre-construction and construction phases to review grading plans, address protection of sensitive biological resources, monitor ongoing work, and maintain communications with the Resident Engineer to ensure that issues relating to biological resources are appropriately and lawfully managed. The Biological Monitor will perform the following duties:

a. Perform a minimum of three focused surveys, on separate days, to determine the presence of gnatcatcher or vireo nest building activities, egg incubation activities, or brood rearing activities within 500 feet of project construction proposed during the breeding season (February 15-September 15). The surveys will begin a maximum of 7 days prior to project construction and one survey will be conducted the day immediately prior to the initiation of work. Additional surveys will be done once a week during project construction in the breeding season. These additional surveys may be suspended as approved by the CFWO. EPA/USIBWC will notify the CFWO at least 7 days prior to the initiation of surveys and within 24 hours of locating any gnatcatchers or vireos.

b. If an active gnatcatcher or vireo nest is found within 500 feet of project construction, the Biological Monitor will report the nest(s) to EPA/USIBWC and the CFWO. After initial identification of the nest, the biological monitor will not approach within 25 feet of an active nest; nest monitoring will occur with binoculars.

Signage will be installed to deter people from entering any area with an active gnatcatcher or vireo nest. The Biological Monitor will use the distance to the project limits and local topography to determine if construction activities are likely to significantly disturb nesting activities. Where disturbance of any gnatcatcher or vireo nest(s) is likely, EPA/USIBWC will contact the CFWO to discuss further measures to avoid the likelihood of nest disturbance, such as: (i) temporarily halting construction activities within 500 feet until the nest naturally fails or fledglings have dispersed; (ii) noise monitoring and noise reducing measures (e.g., equipment shrouds, noise walls, phasing loud activities adjacent to occupied habitat outside the breeding season); and (iii) a nest monitoring program and schedule acceptable to the CFWO. The Biological Monitor will determine whether bird activity is being disrupted during construction activities. If the Biological Monitor determines that bird activity is being disrupted, EPA/USIBWC will stop work and coordinate with

1 The Biological Monitor will be a trained ornithologist with at least 40 hours of independent gnatcatcher and vireo observation in the field and documented experience of at least 20 hours of locating and monitoring gnatcatcher and vireo nests. If necessary, more than one biologist may be used.

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 8 the CFWO to review the avoidance/minimization approach. Upon agreement as to the necessary revisions to the avoidance/minimization approach, work may resume subject to the revisions and continued nest monitoring. Nest monitoring will continue until the nest naturally fails or fledglings have dispersed, as approved by the CFWO.

c. For clearing/grubbing of suitable gnatcatcher habitat outside the gnatcatcher breeding season, perform a minimum of three focused preconstruction surveys, on separate days, to determine the presence of gnatcatchers in the project impact footprint. Surveys will begin a maximum of 30 days prior to performing vegetation clearing/grubbing, and one survey will be conducted the day immediately prior to the initiation of vegetation clearing. If any gnatcatchers are found in the project impact footprint, the Biological Monitor will direct construction personnel to begin vegetation clearing/grubbing in an area away from the gnatcatchers. It will be the responsibility of the Biological Monitor to ensure that gnatcatchers will not be injured or killed by vegetation clearing/grubbing. The Biological Monitor will record the number and location of gnatcatchers disturbed by vegetation clearing/grubbing. EPA/USIBWC will notify the CFWO at least 7 days prior to vegetation clearing/grubbing to allow the CFWO to coordinate with the Biological Monitor on potential bird flushing activities.

d. Oversee installation of and inspect the construction fencing and erosion control measures a minimum of once per week to ensure that any breaks in the fencing or erosion control measures are repaired immediately.

e. Periodically monitor the work area to ensure that work activities do not generate excessive amounts of dust.

f. Train all contractors and construction personnel on the biological resources associated with the project and ensure that training is implemented by construction personnel. At a minimum, training will include: (i) the purpose for resource protection; (ii) a description of the gnatcatcher, vireo, and their habitats; (iii) the conservation measures that should be implemented during project construction to conserve the gnatcatcher and vireo, including strictly limiting activities, vehicles, equipment, and construction materials to the fenced project footprint to avoid sensitive resource areas in the field (i.e., avoided areas delineated on maps or on the project site by fencing); (iv) environmentally responsible construction practices; (v) the protocol to resolve conflicts that may arise at any time during the construction process; and (vi) the general provisions of the Act.

g. Request that the Resident Engineer halt work, if necessary, and confer with the CFWO to ensure the proper implementation of species and habitat protection measures. The Biological Monitor will report any non-compliance issue to the CFWO within 24 hours of its occurrence.

h. Monitor the project site immediately prior to and during construction (at least monthly) to identify the presence of invasive weeds and recommend measures to

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 9 avoid their inadvertent spread in association with the project. Such measures may include inspection and cleaning of construction equipment and use of eradication strategies.

i. Submit email reports (weekly during the breeding season and monthly during the non-breeding season), including photographs of impact areas, to the CFWO during clearing of, and construction within, 500 feet of gnatcatcher or vireo habitat. The reports will document that authorized impacts were not exceeded and general compliance with all conditions. The reports will also outline the location of construction activities, the type of construction that occurred, and equipment used.

These reports will specify numbers, locations, and sex of gnatcatchers or vireos (if observed), their observed behavior (especially in relation to construction activities), and remedial measures employed to avoid and minimize impacts to these species. Raw field notes should be available upon request by the CFWO.

j. Submit a final report to the CFWO within 60 days of completion of project construction that includes: photographs of habitat areas that were to be avoided and other relevant summary information documenting that authorized impacts were not exceeded and that general compliance with all conservation measures was achieved. Provide as-built construction drawings with an overlay of habitat that was impacted and avoided once they have been completed.

CM 2. EPA/USIBWC will temporarily fence (with silt barriers) the limits of project impacts (including staging areas and access routes) to prevent additional impacts and the spread of silt from the construction zone into adjacent avoided habitats. Fencing will be installed in a manner that does not impact avoided habitats. EPA/USIBWC will submit to the CFWO for approval, at least 2 days prior to initiating project impacts, photographs that show the fenced limits of impact. If work occurs within habitat for listed species beyond the fenced/marked limits of impact, all work will cease until the problem has been remedied to the satisfaction of the CFWO. Any impacts to habitat for listed species that occur beyond the approved fence will be offset as determined by the Service. Temporary construction fencing will be removed upon project completion.

CM 3. EPA/USIBWC will confine all heavy equipment, vehicles, and construction activities to existing access roads, road shoulders, and disturbed/developed or designated work areas. Work areas will be limited to what is necessary for construction.

CM 4. All materials imported into the project footprint (e.g., straw wattles, gravel, and mulch) will be obtained from sources that are free of noxious weeds to be confirmed through periodic inspections conducted by the Biological Monitor.

CM 5. Wash stations will be set up at all vehicle entrances into the project footprint to remove plant material, mud, and dirt from vehicles before entering the project footprint.

Sediment accumulated from the washing will be removed daily and placed in a sealed container for disposal in an approved landfill. Project workers will use boot brushes, a metal scraper, soap, water, and scrub brushes to remove mud, debris, and plant materials found on their clothing and personal equipment.

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 10

CM 6. Best management practices (BMPs) for erosion control, stormwater runoff, hazardous material handling, and stockpile management will be implemented to prevent pollution caused by construction operations and to reduce contaminated stormwater runoff.

CM 7. All construction equipment will be inspected for leaks prior to being brought onsite. All equipment shall be well maintained and inspected daily while onsite to prevent leaks of fuels, lubricants or other fluids into wetlands and waterways.

CM 8. Service and refueling procedures will be conducted in a designated area where there is no potential for fuel spills to seep or wash into waterways.

CM 9. No pets, hunting, open fires (such as barbecues), or firearms will be permitted at the project site.

CM 10. Project lighting will be of the lowest illumination necessary for safety and will be directed toward the construction area and away from sensitive habitats, as feasible.

Light glare shields will be used to reduce the extent of illumination into sensitive habitats. In particular, lighting that causes direct illumination into sensitive habitats (e.g., riparian and coastal sage scrub) will be avoided during the period from one hour past sunset through one hour before sunrise.

CM 11. Ground disturbance and vegetation removal will not exceed the minimum amount necessary to complete work at the site.

CM 12. All areas where revegetation is required will be replanted with native species. A native plant restoration and monitoring plan will be developed by a qualified botanist in coordination with the CFWO.

CM 13. Erosion control materials will be installed per manufacturing material specifications and must not contain monofilament netting. Only tightly woven netting or similar material will be used for all geo-synthetic erosion control materials such as coir rolls and geo-textiles. All non-biodegradable erosion control materials will be removed following project completion.

CM 14. All construction personnel will visually check for wildlife on or beneath vehicles and construction equipment before moving or operating them.

CM 15. If listed wildlife is observed within the work area or its immediate vicinity, work will stop until the animal leaves the area of its own volition. The animal will not be harried or harassed into leaving the area. If the animal does not leave of its own accord, the project biologist will be contacted for further guidance.

CM 16. During project activities, all trash will be properly contained in covered garbage receptacles. Following construction, all trash and construction debris from project sites will be removed.

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 11

CM 17. Impacts from fugitive dust during construction will be avoided and minimized through limiting vehicle speeds to 20 miles per hour, controlling vehicle access, watering, and other appropriate measures.

Vireo and its Critical Habitat

CM 18. EPA/USIBWC will prepare a groundwater monitoring plan in coordination with the CFWO. The plan will include collection of year-round groundwater depths within or adjacent to vireo habitat for at least 3 years prior to operation of the APTP and 7 years following the start of APTP operation. The draft plan will be submitted to the CFWO for review and approval prior to APTP construction. Annual reports will be prepared and submitted to the CFWO for review. If monitoring shows that groundwater depths are lower than baseline depths following operation of the APTP, EPA/USIBWC will coordinate with the CFWO to determine if additional consultation is needed.

CM 19. EPA/USIBWC will implement an invasives removal program within the 27.5-acre area within IBWC property west of Dairy Mart Road bridge (Figure 6). EPA/IBWC will submit a draft invasive management plan for the 27.5-acre area to the CFWO for review and approval prior to construction of the APTP. The draft plan will include updated vegetation mapping that will quantify the area dominated by invasive species (i.e., Cal- IPC Ranking of High, Moderate, or Limited), a proposed removal and maintenance schedule, and identification of a funding source for annual maintenance. Annual reports will be submitted to the CFWO by December 1 each year for the operational life of the project.

CM 20. EPA/USIBWC will implement one of the following measures to contribute to vireo conservation and recovery:

a. Provide funding for implementation of 13.5 acres of the County of San Diego’s ISRRP, specifically for invasives removal and riparian restoration in Phase 4 immediately downstream of USIBWC’s property (Figure 7). Proof of funding for

13.5 acres of the ISRRP will be provided to the CFWO prior to construction of the APTP. Implementation of 13.5 acres of riparian restoration will occur at least 2 years prior to APTP operation.

b. Conduct alternative conservation and recovery actions that would provide equivalent benefit to the vireo as CM20a (e.g., habitat enhancement or restoration, cowbird trapping), as approved by the CFWO.

c. Implement a combination or CM20a and CM20b, as approved by the CFWO.

CM 21. EPA/IBWC will fund vireo surveys of suitable habitat within the Tijuana River Valley, including one year prior to APTP operation and every 3 years following APTP operation for 9 years (4 years of surveys total). Survey results will be submitted to the CFWO.

EPA/IBWC will coordinate with the CFWO if surveys detect any significant decreases in the overall vireo population within the Tijuana River Valley to determine if reinitiation of consultation is needed.

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 12

CM 22. EPA/USIBWC will fund vireo surveys of suitable habitat within the Tijuana River Valley, including one year prior to APTP operation and every 3 years following APTP operation for 9 years (4 years of surveys total). Survey results will be submitted to the CFWO. EPA/USIBWC will coordinate with the CFWO if surveys detect any significant decreases in the overall vireo population within the Tijuana River Valley to determine if reinitiation of consultation is needed.

CM 23. Habitat restoration and enhancement activities within the riparian restoration areas will occur outside the vireo breeding season (March 15 to September 15), to the maximum extent practicable. If restoration activities within the restoration areas potentially occupied by vireos is necessary between March 15 and September 15, a qualified vireo biologist2 approved by the CFWO will survey for vireos within the restoration areas, access paths to them, and other areas susceptible to disturbances by restoration activities.

Surveys will consist of three visits separated by 2 weeks starting March 15 of each maintenance/monitoring year. Restoration work will be allowed to continue on the site during the survey period. However, if vireos are found during any of the visits, EPA/USIBWC will notify and coordinate with the CFWO to identify measures to avoid and/or minimize effects to the vireo (e.g., nests and an appropriate buffer will be flagged by the biologist and avoided by the maintenance work).

Ridgway’s Rail

CM 24. EPA/USIBWC will implement one of the following measures to contribute to Ridgway’s rail conservation and recovery:

a. Conduct tamarisk removal within 26 acres of the Tijuana River National Estuarine Research Reserve (Figure 8, or the areas determined by updated vegetation mapping to be the most advantageous for salt marsh restoration), including the following:

i. A draft habitat enhancement and management plan will be submitted to the CFWO and approved prior to APTP construction. The plan will include updated surveys to determine the areas of Tamarisk infestation within potential salt marsh habitat, coordination with the U.S. Navy and Tijuana Slough National Wildlife Refuge if any restoration areas and access to those areas are proposed on their lands, restoration with appropriate native species in any areas above the tidal zone, and long-term maintenance and monitoring (i.e., for the operational life of the project). Implementation will occur at least 2 years prior to APTP operation.

ii. EPA/USIBWC will prepare a long-term management plan for the tamarisk removal areas. A draft plan will be submitted to the CFWO for review and approval prior to construction of the APTP. The plan will include: (1) a Property Analysis Record (PAR) (Center for Natural Lands Management

2 The vireo biologist will be a trained ornithologist with at least 40 hours of independent vireo observation in the field and documented experience of at least 20 hours of locating and monitoring vireo nests. If necessary, more than one biologist may be used

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 13

©1998) or similar cost estimation methods to determine the cost of annual maintenance for the operational life of the project, and (2) a proposed entity that will implement annual maintenance and monitoring activities.

EPA/USIBWC will provide funding of an amount approved by the CFWO based on the PAR for implementation of the long-term management plan. The funding source and time period will be finalized prior to construction of the

APTP.

b. Conduct alternative conservation and recovery actions that would provide equivalent benefit to the Ridgway’s rail as CM24a (e.g., habitat enhancement or restoration, contribution to the Ridgway’s Rail Recovery Fund at The San Diego Foundation), as approved by the CFWO.

c. Implement a combination or CM24a and CM24b, as approved by the CFWO.

CM 25. Habitat restoration and enhancement activities within tamarisk removal areas will occur outside the Ridgway’s rail breeding season (March 15 to September 15), to the maximum extent practicable. If restoration activities within the restoration areas potentially occupied by Ridgway’s rail is necessary between February 15 and September 15, a qualified Ridgway’s rail biologist3 approved by the CFWO will survey for Ridgway’s rail within the restoration areas, access paths to them, and other areas susceptible to disturbances by restoration activities. Surveys will consist of three visits separated by 2 weeks starting March 15 of each maintenance/monitoring year. Restoration work will be allowed to continue on the site during the survey period. However, if Ridgway’s rail are found during any of the visits, EPA/USIBWC will notify and coordinate with the CFWO to identify measures to avoid and/or minimize effects to the Ridgway’s rail (e.g., nests and an appropriate buffer will be flagged by the biologist and avoided by the maintenance work).

Gnatcatcher

CM 26. Clearing of coastal sage scrub will occur outside the gnatcatcher nesting season (February 15 to August 31, or sooner if the Biological Monitor demonstrates to the satisfaction of the CFWO that there are no active gnatcatcher nests within 500 feet of the vegetation removal area).

Quino

CM 27. A qualified biologist4 will conduct a preconstruction survey for Quino host plants in areas of suitable habitat that may be impacted by construction, including staging areas, during appropriate blooming periods (to ensure host plants are correctly identified) no

3 The Ridgway’s rail biologist will be a trained ornithologist with at least 40 hours of independent Ridgway’s rail observation in the field and documented experience of at least 20 hours of locating and monitoring Ridgway’s rail during the breeding season. If necessary, more than one biologist may be used.

4 The qualified biologist for this CM will be familiar with Quino life history and habitat requirements and have documented experience surveying for and detecting Quino host plants.

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 14 less than one year prior to construction within each project footprint. If Quino host plants are detected within the project area, EPA/USIBWC will coordinate with the Service on appropriate avoidance and minimization measures that can be implemented and to determine if additional consultation is needed.

Vernal Pools

CM 28. A seasonally appropriate, focused survey for seasonal pools will be conducted in each project footprint no less than two years prior to construction of each project. If any seasonal pools are found, they will be flagged and fully avoided. If full avoidance is infeasible, focused protocol surveys for San Diego fairy shrimp will be conducted. If San Diego fairy shrimp are detected in any seasonal pools that cannot be completely avoided, EPA/USIBWC will request reinitiation of section 7 consultation with the Service.

Listed Plants

CM 29. Focused surveys for federally listed plant species with the potential to occur in the project area will be conducted during appropriate blooming periods and no less than one year prior to construction within each project site. The surveys will follow the Guidelines for Conducting and Reporting Botanical Inventories for Federally Listed, Proposed and Candidate Plants (USFWS 2000) and Protocols for Surveying and Evaluating Impacts to Special Status Native Plant Populations and Sensitive Natural Communities (California Department of Fish and Wildlife [CDFW] 2018). If federally listed plants are found, EPA/USIBWC will coordinate with the Service on appropriate avoidance and minimization measures that can be implemented and to determine if additional consultation is needed.

BASELINE CONDITIONS

Project Site and Surrounding Conditions

The existing ITP parcel sits adjacent to the Tijuana River just downstream of the international border.

Upstream of the border and ITP parcel, the Tijuana River is confined within a concrete-lined channel through the City of Tijuana up to Rodriquez Dam. Downstream of the border and ITP parcel, Tijuana River flows through an open channel, under the Dairy Mart Road bridge, through a wide and flat floodplain that supports extensive riparian habitat, and eventually flows into the Tijuana Estuary before discharging to the Pacific Ocean. The direct impact areas for the proposed project consist mostly of developed areas, disturbed habitat, and non-native vegetation (Table 1). A small portion of the existing ITP parcel supports a patch of mulefat surrounded by development. Another small area within the potential impact area for Project B in Smuggler’s Gulch supports mulefat and coastal sage scrub.

Transboundary Flows

Under baseline conditions, uncontrolled trash, untreated wastewater, and sedimentation from Tijuana contribute to transboundary flows of sediment and pollution via the Tijuana River and tributary canyons. Transboundary flows have resulted in high bacterial and pollutant concentrations in the

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 15

Tijuana River on the U.S. side of the border and sedimentation that can reduce flow capacity of the river and tidal flow exchange in the estuary.

Transboundary flows are also a source of freshwater that currently enters the Tijuana River Valley and Tijuana Estuary. Between 2016 and 2021, an average of 22,871 million gallons per year flowed across the border in the Tijuana River. As described in the Project Description section, transboundary flows occur when PB-CILA is shut down or flow rates exceed its capacity (23 MGD during the 2016-2021 date range), such as during and immediately after significant precipitation. Because PB- CILA shuts down during and following precipitation, the majority of the transboundary flows that PB-CILA diverts are during dry-weather days or towards the end of a rain event when flows subside back below 23 MGD. Under baseline conditions, transboundary flows occur an average of 189 days per year (2017 to 2020), or 15 days per month (2016 to 2021).

Vireo and its Critical Habitat

While not expected to occur within the direct project footprint, vireo have consistently been detected in the riparian area of Smuggler’s Gulch adjacent to the footprint for part of Project B (URS 2009a) and in the riparian habitat downstream of the project in the Tijuana River Valley (Kus 2022). The Tijuana River Valley supports an important vireo population, which generally occurs within the riparian forest and riparian scrub between Dairy Mart Road and Tijuana Estuary. The drainage-wide population was estimated to be about 113 territories in 2004 (Howell and Kus 2018), 88 territories in 2017 (Howell and Kus 2018), and 148 territories in 2020 (Kus 2022) (Figure 7). The vireo population in the Tijuana River Valley declined following the invasion of riparian habitat by the invasive Kuroshio shot hole borer (KSHB), which was first detected in 2015 (Boland 2016). In the years following the KSHB invasion, riparian habitat has rebounded in most areas. However, invasive species such as Arundo donax have increased significantly and prevented reestablishment of suitable vireo habitat in some areas, particularly just west of Dairy Mart Road.

The physical and biological features (PBFs)5 of designated critical habitat for the vireo include habitat features that support vireo feeding, nesting, roosting, and sheltering. These PBFs are described in the critical habitat designation as riparian woodland vegetation that generally contains both canopy and shrub layers and includes some associated upland habitats (Service 1994). The critical habitat designation also states that the portion in Tijuana River Valley specifically supports riverine and floodplain habitats (particularly willow-dominated riparian woodland with dense understory vegetation maintained, in part, in a non-climax stage by periodic floods or other agents) and adjacent coastal sage scrub, chaparral, or other upland plant communities. Tijuana River Valley supports about 879 acres of designated critical habitat for vireo.

Ridgway’s Rail

Suitable habitat for Ridgway’s rail does not occur in the direct project footprint. However, Tijuana Estuary downstream of the project supports about 720 acres of saltmarsh occupied by Ridgway’s rail, including about 74 acres of cordgrass (Spartina foliosa). Ridgway’s rails in Tijuana Estuary occur

5 The designation of critical habitat for vireo uses the term primary constituent element. The new critical habitat regulations (81 FR 7214) replace this term with PBFs. This shift in terminology does not change the approach used in conducting our analysis. In this consultation, we use the term PBFs to mean primary constituent elements.

Lily Lee and Gilbert Anaya (22-0014986-S7-I_SD) 16 mostly in cordgrass (low marsh habitat), but also occupy mid and high marsh habitat (Zembal and Massey 1981). The Tijuana Estuary population can fluctuate significantly between breeding seasons but is generally one of the largest populations in the U.S. species range. Population highs occurred in 2007 (142 pairs) and 2016 (127 pairs). The lowest population count since the 1980s was detected in 2019 (29 pairs) following a prolonged closure of the river mouth coinciding with significant transboundary flows of untreated wastewater, which resulted in flooding and anoxic conditions in the estuary. Between 2020 and 2022, focused surveys detected an estimated 73-94 pairs in Tijuana Estuary and much lower numbers in other historically large populations like Upper Newport Bay and Seal Beach National Wildlife Refuge, making Tijuana Estuary the largest population for the last 3 years (Zembal and Hoffman 2022). In 2023, focused surveys detected an estimated 70 pairs of Ridgway’s rails in Tijuana Estuary, which did not include any habitat south of the river channel (Zembal pers. comm. 2023).

Gnatcatcher

Suitable habitat for gnatcatcher in the direct project footprint consists of a small amount (about 0.2 acre) of coastal sage scrub in Smuggler’s Gulch that could be temporarily impacted by Project B.

Gnatcatchers are known to occur in the hills to the west of Smuggler’s Gulch and along the slopes on the east side of Smuggler’s Gulch (URS 2009b, Balk Biological Inc 2018). Gnatcatchers have also been detected in the hills south of Project B’s footprint along Monument Road (Dudek 2019).

Quino

No suitable habitat or Quino host plants (i.e., Plantago erecta) were detected in the direct project footprint during project surveys. Quino have been detected in the hills of the Nelson Sloan Quarry site about 0.4 mile west of the ITP parcel (Dudek 2021). The Nelson Sloan Quarry supports large amounts of P. erecta, which decreases in abundance as the slopes of the site flatten out toward Monument Road.

San Diego Fairy Shrimp

No suitable habitat for San Diego fairy shrimp was detected in the project footprint during project surveys in 2021. However, surveys occurred during a time period when seasonal pools may not have been ponded and are more difficult to detect. If seasonal pools occur at the project site, the potential exists that they may be occupied by San Diego fairy shrimp. San Diego fairy shrimp are known to occur just east of Oneonta Slough about 2.5 miles northwest of the project site.

Listed Plant Species

Salt marsh bird’s beak is a hemiparasite that generally occurs on high marsh plant species (e.g., Distichlis spicata and Distichlis littoralis) in areas subject to intermittent disturbance.