`State Water Resources Control Board
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`May 21, 2025
`Mr. Bryan Kelly, Deputy General Manager
`Merced Irrigation District
`744 W. 20th Street
`Merced, CA 95340
`Sent via email: bkelly@mercedid.org
`Merced River Hydroelectric Project and Merced Falls Hydroelectric Project
`Federal Energy Regulatory Commission Project Nos. 2179 and 2467
`Merced and Mariposa Counties
`Merced River and Tributaries
`STATE WATER RESOURCES CONTROL BOARD STAFF COMMENTS ON MERCED
`IRRIGATION DISTRICT’S NOTICE OF PREPARATION OF A DRAFT
`ENVIRONMENTAL IMPACT REPORT FOR THE MERCED RIVER AND MERCED
`FALLS HYDROELECTRIC PROJECTS
`Dear Mr. Kelly:
`On April 21, 2025, Merced Irrigation District (Merced ID) issued a Notice of Preparation
`(NOP) of a Draft Environmental Impact Report (Draft EIR) to satisfy the California
`Environmental Quality Act (CEQA) requirements for the Federal Energy Regulatory
`Commission (FERC) relicensing of its Merced River Hydroelectric Project (Merced River
`Project, FERC Project No. 2179) and Merced Falls Hydroelectric Project (Merced Falls
`Project, FERC Project No. 2467) (collectively Merced Projects). The NOP includes a 30-
`day public review period and requests comments by 2:00 p.m. on May 21, 2025.
`Background on Water Quality Certification and CEQA Processes
`Merced ID owns and operates the Merced Projects located in the Merced River
`watershed in Merced and Mariposa counties, California. The Merced Projects consist of
`two developments, New Exchequer (Merced River Project) and McSwain (Merced Falls
`Project).
`The State Water Resources Control Board (State Water Board or Board) previously
`received water quality certification (certification) applications for the Merced Projects
`from Merced ID pursuant to section 401 of the Federal Clean Water Act (CWA)
`(33 U.S.C. § 1341) on April 15, 2024. The applications for certification were associated
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`Mr. Bryan Kelly May 21, 2025
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`with the decision by the United States Court of Appeals for the Ninth Circuit (Ninth
`Circuit) in California State Water Resources Control Board v. FERC.1
`On March 18, 2025, Merced ID withdrew its certification applications for the Merced
`Projects and on March 21, 2025, advised FERC of its intent to reapply for certification
`by April 30, 2025. In its March 2025 notice to FERC regarding its withdrawal of the
`certification applications for the Merced Projects, Merced ID cited the need for additional
`information and a supplemental analysis Merced ID planned to complete to clarify its
`applications for certification, including completion of the environmental review pursuant
`to CEQA.
`Prior to Merced ID’s withdrawal of the Merced Projects’ certification applications,
`relicensing of the Merced Projects had reached several key milestones including:
`(1) Merced ID’s issuance of a Notice of Availability (NOA)2 for a Notice of Intent (NOI) to
`rely on FERC’s 2015 Final Environmental Impact Statement for the Merced Projects
`(2015 Final EIS) with mandatory conditions in combination with a Supplemental
`Analysis to satisfy CEQA requirements for the Merced Projects; (2) Merced ID’s release
`of a draft Initial Study/Mitigated Negative Declaration (IS/MND) for public comment and
`issuance of Merced ID’s NOI3 to adopt an IS/MND as a supplement to FERC’s 2015
`Final EIS to satisfy CEQA requirements for the FERC relicensing of the Merced
`Projects; and (3) the Board’s public release of a draft certification for the Merced
`Projects on January 27, 2025, and Merced ID’s submittal of comments on the draft
`certification on February 28, 2025.
`On April 14, 2025, Merced ID requested a pre-filing meeting with the State Water Board
`pursuant to the United States Environmental Protection Agency’s (USEPA) regulation
`governing CWA section 401 water quality certifications. (40 CFR 121.4.) State Water
`Board staff met with Merced ID representatives on April 25, 2025, to discuss
`Merced ID’s plan to submit new certification applications for the relicensing of the
`Merced Projects and Merced ID’s intention to develop an Environmental Impact Report
`to satisfy its CEQA requirements by supplementing FERC’s 2015 Final EIS. Merced ID
`submitted new applications for certification to the State Water Board for the relicensing
`of the Merced Projects on May 15, 2025.
`State Water Board staff attended a virtual scoping meeting for the Merced Projects
`hosted by Merced ID on May 7, 2025. State Water Board staff are submitting the
`enclosed comments pertaining to Merced ID’s NOP of a Draft EIR for the relicensing of
`the Merced Projects: Comments on Notice of Preparation of a Draft Environmental
`Impact Report for Relicensing of the Merced River and Merced Falls Hydroelectric
`Projects.
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`1 43 F.4th 920 (9th Cir. 2022), cert denied 2023 WL 3440583 (Westlaw 2023).
`2 State Water Board staff provided comments on Merced ID’s May 29, 2024 NOA on
`June 27, 2024.
`3 State Water Board staff provided comments on Merced ID’s February 13, 2025 NOI on
`March 14, 2025.
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`Mr. Bryan Kelly May 21, 2025
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`If you have questions regarding this letter please contact Bryan Muro, State Water
`Board Project Manager for the Merced Projects , by email to:
`Bryan.Muro@waterboards.ca.gov or by phone call to: (916) 327-8702. Written
`correspondence should be directed to:
`State Water Resources Control Board
`Division of Water Rights – Water Quality Certification Program
`Attn: Bryan Muro
`P.O. Box 2000
`Sacramento, CA 95812-2000
`Sincerely,
`Bryan Muro
`Water Resources Control Engineer
`Water Quality Certification Program
`Division of Water Rights
`Enclosure: Comments on Notice of Prepar ation of a Draft Environmental Impact
`Report for Relicensing of the Merced River and Merced Falls
`Hydroelectric Projects
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`Mr. Bryan Kelly May 21, 2025
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`ec: Debbie-Anne Reese, Secretary
`Federal Energy Regulatory Commission
`Via e-filing
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`Patrick Pulupa, Executive Officer
` Central Valley Regional Water Quality Control Board
` Email: Patrick.Pulupa@waterboards.ca.gov
`Matt Scroggins, Senior Water Resource Control Engineer
`Central Valley Regional Water Quality Control Board
`Email: Matt.Scroggins@waterboards.ca.gov
`James Lynch, Principal Consultant
`HDR Engineering, Inc.
`Email: Jim.Lynch@hdrinc.com
`Mary Mahoney, Project Coordinator
`HDR Engineering, Inc.
`Email: Mary.Mahoney@hdrinc.com
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`Enclosure: Comments on Notice of Preparation of a Draft Environmental Impact Report
`for Relicensing of the Merced River and Merced Falls Hydroelectric Projects
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`State Water Resources Control Board (State Water Board or Board) staff are providing
`the following comments on Merced Irrigation District’s (Merced ID) Notice of Preparation
`of a Draft Environmental Impact Report for the relicensing of the Federal Energy
`Regulatory Commission (FERC) relicensing of the Merced River Hydroelectric Project
`(Merced River Project, FERC Project No. 2179) and Merced Falls Hydroelectric Project
`(Merced Falls Project, FERC Project No. 2467) (collectively Merced Projects). The
`Notice of Preparation (NOP) notes Merced ID’s plan to satisfy its California
`Environmental Quality Act (CEQA) requirements for the relicensing of the Merced
`Projects through an Environmental Impact Report (EIR) and FERC’s 2015 Final
`Environmental Impact Statement for the Merced River and Merced Falls Hydroelectric
`Projects (2015 Final EIS).
`1. In California, the State Water Board is responsible for protecting the State’s
`water quality, including through the issuance of a Clean Water Act, Section 401
`water quality certification (certification). Certification must ensure compliance with
`water quality standards and other appropriate requirements of state law, such as
`water quality control plan standards. Certification is required before FERC can
`issue a project license. If the State denies certification, FERC cannot issue the
`license for the project. If the State issues certification with conditions, those
`conditions become conditions of the federal license for the project.
`On March 18, 2025, Merced ID withdrew its April 15, 2024 certification
`applications for the Merced Projects and noted additional information and a
`supplemental analysis were needed to clarify its applications for certification,
`including completion of the environmental review pursuant to CEQA. On
`May 15, 2025, Merced ID submitted new applications to the State Water Board
`for certification for the Merced Projects.
`State Water Board staff would like to emphasize that the CEQA analysis in the
`EIR should include all the relevant changes to the Merced Projects since
`issuance of FERC’s 2015 Final EIS and the State Water Board should be given
`ample time to review the Final EIR prior to the certification action date, which is
`May 15, 2026.
`2. Separately from the Merced Projects relicensing process, Merced ID is
`developing a Recreation Facilities Improvement Project (Recreation Project)
`Draft Programmatic Environmental Impact Report (Recreation DPEIR),
`SCH# 2024051222, which had a public review period ending on March 9, 2025.
`The Recreation Project is a separate project encompassing only a portion of the
`Merced Projects. Therefore, reliance on the Recreation Project’s CEQA
`document in the Draft EIR will only cover certain elements of the Merced Projects
`and therefore does not comprehensively satisfy CEQA requirements for the
`Merced Projects FERC relicensing.
`3. Section 4.17 of the NOP states the Draft EIR will identify reasonable alternatives
`to the Merced Projects that might reasonably reduce significant impacts. One of
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`Enclosure: Comments on Notice of Preparation of a Draft Environmental Impact Report
`for Relicensing of the Merced River and Merced Falls Hydroelectric Projects
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`the proposed alternatives anticipates reviewing the Merced Projects with
`conditions from FERC’s 2015 Final EIS and the State Water Board’s
`January 27, 2025, draft certification.1 State Water Board staff agrees that review
`and analysis of the conditions of the January 2025 draft certification for the
`Merced Projects is appropriate.
`4. Currently, Merced ID is the largest water user in the Merced River watershed and
`owns and operates, in coordination with the Merced Projects, dams that are
`migration barriers to salmon and steelhead. The State Water Board’s 2018
`Substitute Environmental Documents for the Lower San Joaquin River and
`Southern Delta2 (SED) and NMFS’ Recovery Plan for the Evolutionary Significant
`Units of Sacramento River Winter-run Chinook Salmon and Central Valley
`Spring-run Chinook Salmon and the Distinct Population Segment of California
`Central Valley Steelhead (NMFS 2014) detail how the combination of water use
`and migration barriers are known to have caused significant negative effects to
`native fish species in the Merced River watershed. As described in the State
`Water Board’s 2018 SED, the San Joaquin River Basin once supported large
`spring-run and fall-run (and possibly late fall-run) Chinook salmon populations;
`however, it is widely thought that the basin now only supports fall-run Chinook
`salmon populations, and these populations are facing a high risk of extinction.
`The Stanislaus, Tuolumne, and Merced rivers (individually or combined) have
`had larger reductions in the natural production of adult fall-run Chinook salmon
`than any of the other tributaries (or combination of three tributaries) to the
`Sacramento or San Joaquin rivers when comparing the 1967-1991 and 1992-
`2011 time periods.
`State Water Board staff request Merced ID’s CEQA analysis includes a range of
`alternatives or mitigation measures to avoid or substantially lessen the significant
`effects of the Merced Projects and ensure the attainment of water quality
`standards, including the protection of beneficial uses for fish and wildlife, under a
`new FERC license(s). State Water Board staff encourage Merced ID to continue
`to explore infrastructure improvements that can efficiently provide cold water to
`native fish populations or provide native fish migratory access to cold water
`habitats within or above the Merced Projects area. Over the past several years
`there has been a large amount of public funding available for restoration and
`infrastructure improvement projects. While federal and state funding for
`restoration and infrastructure improvement projects may be more limited in the
`future, State Water Board staff encourage Merced ID to explore any and all
`federal and state funding opportunities that could help mitigate the impacts the
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`1 On January 27, 2025, the State Water Board released for public comment a draft
`certification for the Merced Projects; the comment period ended on February 28, 2025.
`2 The SED for the 2018 Bay-Delta Plan can be accessed at the following address:
`https://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/bay_delt
`a_plan/water_quality_control_planning/2018_sed/
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`Enclosure: Comments on Notice of Preparation of a Draft Environmental Impact Report
`for Relicensing of the Merced River and Merced Falls Hydroelectric Projects
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`Merced Projects have on native fish and wildlife. Given that the Board must
`ensure through the issuance of certification that the Merced Projects will comply
`with water quality standards and other appropriate requirements of state law,
`Merced’s Draft EIR should identify and analyze what actions will be implemented
`and alternatives thereto to ensure the Merced Projects comply with water quality
`standards and protect beneficial uses.
`5. The Merced River is listed as impaired under Clean Water Act section 303(d) for
`elevated temperature. Merced ID’s CEQA analysis in the Draft EIR should
`evaluate the potential environmental impacts of operating Lake McClure at
`relatively low storage levels and higher storage levels during the term of a new
`FERC license(s) to help address this temperature impairment. Storage levels
`near the end of the irrigation season that are less than 300,000 acre-feet are
`known to contribute to harmful and lethal water temperatures in the Merced River
`in areas used by salmon and steelhead. The effect of low reservoir storage on
`water temperature is particularly noticeable in the months of September through
`November during the Chinook salmon spawning season. As illustrated in
`Figure F.1.6-7a and elsewhere in Appendix F.1 of the State Water Board’s 2018
`SED, Lake McClure storage volumes affect the temperature of water released
`from the reservoir.
`The water temperature impacts associated with releases from Lake McClure
`extend downstream and are amplified as water temperature increases at
`additional dam complexes, until the water is released below Crocker-Huffman
`diversion dam, the current limit of anadromy on the Merced River. Warm water
`releases are most acute in the fall (i.e., during September through November)
`when adult salmon are migrating into the Merced River and spawning. Further,
`Figure 19-7 of Chapter 19 of the State Water Board’s 2018 SED shows that the
`water temperatures necessary for spawning salmon (i.e., less than 55.4 degrees
`Fahrenheit [°F]) are delayed by approximately one month on average during the
`fall-run Chinook salmon spawning period when comparing Lake McClure inflow
`temperatures to Crocker-Huffman diversion dam release temperatures. This
`approximately one-month delay in access to optimal spawning temperatures
`likely affects egg viability and shortens the overall window of opportunity
`available to juvenile salmon for successful development and migration prior to
`ocean entry. Merced ID’s Draft EIR needs to analyze the environmental impacts
`of potential changes that may be needed to existing operations in order to
`address existing water quality impairments and impacts to beneficial uses
`associated with Merced ID’s reservoirs.
`The impact of the Merced Projects on beneficial uses and water quality
`objectives (e.g., temperature) is applicable to the questions of compliance with
`water quality standards/water quality control plans. As a result, State Water
`Board staff request Merced ID perform this analysis, along with appropriate
`alternatives that would achieve compliance with water quality standards, in the
`Merced Projects’ Draft EIR.
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`Enclosure: Comments on Notice of Preparation of a Draft Environmental Impact Report
`for Relicensing of the Merced River and Merced Falls Hydroelectric Projects
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`6. Previously, Merced ID relied heavily on FERC’s 2015 Final EIS analysis to
`support proposed flow alternatives for Merced Projects’ operations under a new
`FERC license(s). Due to when FERC’s 2015 Final EIS was developed, Tables 3-
`9 and 3-10 of FERC’s 2015 Final EIS, which provide targeted, proposed, and
`recommended minimum instream flow requirements, did not include any analysis
`of potential environmental impacts from possible changes to the Merced Projects
`needed to ensure compliance with the 2018 Update of the Water Quality Control
`Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Watershed (2018
`Bay-Delta Plan Update).
`In 2018, the State Water Board’s Bay-Delta Plan was updated to include flow
`objectives for the Merced River. The 2018 Bay-Delta Plan Update states:
`“Maintain 40% of unimpaired flow, with an allowed adaptive range between 30%
`- 50%, inclusive, from each of the Stanislaus, Tuolumne, and Merced Rivers from
`February through June.” The 2018 Bay-Delta Plan Update was evaluated in
`accordance with CEQA in the Board’s 2018 SED.
`The Merced Projects’ Draft EIR should include an analysis of the environmental
`impacts from changes needed for the Merced Projects coming into compliance
`with the required flows of the Bay-Delta Plan. This may be accomplished by
`pointing to the Board’s SED. Accordingly, State Water Board staff request
`Merced ID’s Draft EIR includes an evaluation of the Merced Projects’ compliance
`with applicable provisions of the 2018 Bay-Delta Plan Update, including separate
`analysis of implementation of the unimpaired flow provisions and any proposed
`voluntary agreements.
`7. Low flow and dry conditions experienced on the Merced River in the summer and
`early fall of 2022 resulted in the river’s disconnection from the mainstem of the
`Lower San Joaquin River. The Board received letters from the National Marine
`Fisheries Service (NMFS), California Department of Fish and Wildlife (CDFW),
`and other parties notifying the Board of the dry river conditions and requesting an
`investigation into the reasons the river went dry along with actions the Board
`should take to prevent the river from going dry in the future.
`The Draft EIR should include analysis of NMFS’s recommended preliminary
`baseflow target of 66 cubic feet per second. State Water Board staff request
`analysis in the Merced Projects’ Draft EIR of NMFS’s recommended baseflow to
`help protect fish passage, ecological processes, and essential fish habitat in the
`lower Merced River and prevent future disconnection of the Merced River with
`the Lower San Joaquin River.
`8. Project activities may have the potential to impact special-status amphibians
`within the Merced Projects’ area of operations. If during the CEQA process,
`Merced ID determines take of listed species is anticipated, or potential impacts to
`the habitat listed species rely on may occur, State Water Board staff request
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`Enclosure: Comments on Notice of Preparation of a Draft Environmental Impact Report
`for Relicensing of the Merced River and Merced Falls Hydroelectric Projects
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`Merced ID include appropriate mitigation measures in the Merced Projects’ Draft
`EIR to ensure protection of the species and their habitats.
`9. In its February 2025 Initial Study/Mitigated Negative Declaration document for
`the Merced Projects FERC relicensing, Merced ID indicated a less-than-
`significant impact on California Central Valley (CCV) steelhead with likely no
`impact on individuals, citing that the implementation of the Staff Alternative With
`Mandatory Conditions analyzed in FERC’s 2015 Final EIS resulted in marginal
`flow increases downstream of the Proposed Project area. Additionally, Merced ID
`cited that analysis within the 2015 Final EIS indicated that this flow would result
`in minor habitat enhancement or no habitat changes. Specifically, analysis of
`impacts for the Staff Alternative With Mandatory Conditions estimated a two
`percent reduction in spawning habitat for CCV steelhead but a three percent
`increase in rearing habitat for fry and two percent increase for rearing habitat for
`juveniles. Water temperatures necessary for smoltification were exceeded 44
`percent of the time, a slight decrease when comparing existing Merced ID
`operations to the Staff Alternative With Mandatory Conditions.
`As stated in Comment 5 above and with respect to water resources, the Clean
`Water Act section 303(d) (33 U.S.C. §1313(d)) listing of the Lower Merced River
`as impaired due to elevated temperature is evidence that the temperature water
`quality objective is not being met downstream of the Merced Projects. The
`segment of the Merced River downstream of McSwain Reservoir to the
`confluence with the San Joaquin River includes beneficial use designations for
`cold freshwater habitat, cold migration, and cold spawning. The 303(d) listing is
`based upon information submitted by CDFW in the form of a report entitled
`“Temperature Water Quality Standards for the Protection of Anadromous Fish in
`the Stanislaus River, Merced River, Tuolumne River, and the San Joaquin River.”
`This report provides an overview of how altered temperature conditions in both
`the San Joaquin River and its major tributaries (including the Merced River) may
`be affecting anadromous fish populations. During the 2011 Merced River 303(d)
`listing review, CDFW states: “[CDFW] believes that one critical factor limiting
`anadromous salmon and steelhead population abundance is high water
`temperatures which exist during critical life stages in the tributaries and the main-
`stem [San Joaquin River]. This results largely from water diversions,
`hydroelectric power operations, water operations and other factors.”
`Additionally, a recent genetics study of Oncorhynchus mykiss (O. mykiss) within
`the Merced River watershed by Pearse and Cambell (2018) found that O. mykiss
`located above Lake McClure retain indigenous ancestry and genetic markers
`associated with anadromy. The study also found that these populations of
`O. mykiss in the upper Merced River watershed likely express an adfluvial life
`history, meaning that they are using Lake McClure instead of migrating to the
`ocean because New Exchequer Dam blocks their migratory route.
`Major diversion facilities, like the Merced Projects, play a significant role in the
`reduction of instream flow downstream of the diversions and should be
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`Enclosure: Comments on Notice of Preparation of a Draft Environmental Impact Report
`for Relicensing of the Merced River and Merced Falls Hydroelectric Projects
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`considered as having a greater impact since the impoundment of water and
`reduction of instream flow contributes to higher water temperatures. For
`example, the temperature of water released from Lake McClure affects water
`temperatures farther downstream, including below Crocker-Huffman diversion
`dam during September through November when adult salmon are migrating into
`the Merced River and spawning. Information provided in Chapter 19 and Master
`Response 3.1 from the State Water Board’s 2018 SED correlates the amount of
`flow in the Merced River below the Merced Projects with water temperatures
`downstream of the Merced Projects. The SED identifies these potential impacts
`that the Merced Projects have on not only CCV steelhead, but also many other
`species in the downstream system. As stated in Comment 1 above, the State
`Water Board is responsible for certifying that the Merced Projects will be
`operated under any new FERC license(s) in a manner that is protective of water
`quality and meets water quality standards, which includes compliance with water
`quality objectives and protection of designated beneficial uses.
`Generally, CEQA defines baseline as the existing conditions when the lead
`agency begins its environmental review. There is no indication that Merced ID
`began its Merced Projects’ CEQA analysis in 2015, and, accordingly, Merced
`ID’s CEQA analysis for the development of the Draft EIR should include updates
`that reflect the current or other appropriate baseline conditions for the Merced
`Projects.
`10. CEQA requires that Merced ID initiate tribal consultation with the appropriate
`tribes within the Merced Projects’ area. State Water Board staff recommend
`Merced ID ensure it obtains an updated list of California Native Tribes from the
`Native American Heritage Commission to ensure the appropriate tribes are given
`the opportunity for consultation pursuant to Public Resources Code section
`21080.3.1, subdivision (c).
`11. The analysis conducted in FERC’s 2015 Final EIS to evaluate potential impacts
`to Chinook salmon spawning and egg incubation relied on Merced ID’s 2013
`Chinook Salmon Egg Viability Study (Technical Memorandum 3-6). However,
`within the 2013 egg viability study, the eggs were not placed in the Merced River
`until November 20, 2012. This start date of the study is concerning because river
`temperatures are typically much warmer at the beginning of the spawning period
`(i.e., mid-October) compared to the end of November when this study started.
`Carcass survey data collected annually on the Merced River shows adult salmon
`typically begin to arrive in the Merced River spawning reaches around mid-
`October of each year, and spawning activity increases dramatically around the
`end of October. State Water Board staff are concerned that the potential impacts
`of the Merced Projects were evaluated using the 2013 egg viability study which
`started late in the spawning season and started at a time when water
`temperatures typically become suitable for spawning. The 2013 egg viability
`study should have started at the beginning of the spawning period to better
`inform the relicensing process. As discussed in Comment 5 above, information in
`the State Water Board’s 2018 SED shows that the Merced Projects contribute to
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`Enclosure: Comments on Notice of Preparation of a Draft Environmental Impact Report
`for Relicensing of the Merced River and Merced Falls Hydroelectric Projects
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`an approximately one-month delay in water temperatures reaching suitable
`spawning thresholds for salmon. State Water Board staff recommend the Draft
`EIR include additional analysis that adequately evaluates potential alternatives to
`the proposed operations of the Merced Projects to address the Merced Projects’
`impacts on water quality (e.g., water temperature) and associated beneficial uses
`(e.g., adult Chinook salmon migration, spawning, and egg incubation). This
`analysis should specifically include alternatives that address protection of
`beneficial uses during this time period.
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