Scott & Shasta Update: Critical Water Quality and Flow Processes Underway
- Amber Jamieson
- 1 day ago
- 4 min read
The Scott and Shasta Rivers, two of the most ecologically and culturally significant tributaries of the Klamath River, are at the center of long-awaited state action. These watersheds—vital for salmon recovery, Tribal lifeways, agriculture, and ecological resilience—are the focus of two important regulatory processes that are currently underway:
emergency minimum instream flow-setting process led by the State Water Resources Control Board (SWRCB) and;
development of Waste Discharge Requirements (WDRs) and updated Total Maximum Daily Loads (TMDLs), led by the North Coast Regional Water Quality Control Board (Regional Board).
Emergency Flow-Setting Process
On October 16, 2024, the SWRCB adopted a resolution directing staff to move forward with an emergency regulation and begin identifying the scientific work needed to establish long-term baseline flows in both watersheds. This includes conducting biological and economic studies to assess the potential impacts of baseline flows. This was prompted by a petition from Karuk Tribe, et al, to adopt minimum instream flows on the Scott River, and a subsequent petition from California Coastkeeper Alliance et al, to adopt minimum instream flows on the Shasta River.
On January 7, 2025, the Board formally re-adopted the emergency regulations to maintain baseline flows in the Scott and Shasta Watersheds while permanent regulations were developed. This regulation is now in effect for one year and may be re-adopted or rescinded depending on drought and flow conditions.
While the recent decision is a positive step forward, river and fish advocates have raised concerns that the regulations need to be more robust, and are calling on the Water Board to conduct the required studies on not only baseline flows but also recovery flows. Baseline flows only provide the bare minimum flows fish need to survive, and would only slow extinction. However, recovery flows aim to improve river conditions so that salmon populations can recover and species listed under the Endangered Species Act, such as coho salmon, are delisted, eventually resulting in a harvestable surplus of salmon.
Emergency minimum instream flows are intended to protect critical habitat for endangered salmon and sustain minimum flows for other beneficial uses, including Tribal subsistence, recreation, fire protection, and ecosystem function. The State Water Board is currently seeking public input to inform the development of scientific and economic analyses that will support long-term flow requirements.
This is a critical opportunity to ensure that flow standards are not weakened by political pressure from commercial operations, but to ensure that the flow standards are informed by the best available science and traditional knowledge, ensuring flows are adequate to promote the recovery of endangered species.
The SONCC Coho Recovery Plan (2014) provides the key stresses and threats to the Interior Klamath diversity stratum of Coho Salmon. In general, stresses are the direct impacts on species’ recovery, and threats are the actions that cause stresses. Both the Scott and Shasta River populations face the same key limiting threats as determined by the SONCC Coho Recovery Plan. These are agricultural practices and dams/diversions. In terms of recovery strategies, the Recovery Plan includes “improved water use management to increase flows” for the Scott River population and to “adjust management to benefit life history requirements of coho” for the Shasta River population. Both strategies call for progress in securing water allocation rights and improving instream flows.
TMDL and Waste Discharge Requirements: Long-Awaited Regulation of Agricultural Pollution
While emergency flows are an immediate fix, the Regional Board is also moving forward with long-term regulatory tools under the Clean Water Act and California Water Code. After years of delay, the Board is developing Waste Discharge Requirements (WDRs) to replace the ineffective voluntary waivers that have been in place since the early 2000s.
This year, the Regional Board initiated the California Environmental Quality Act (CEQA) process to prepare a Draft Environmental Impact Report (EIR) for the regulation of commercial agricultural operations in the Scott and Shasta River watersheds. This includes the release of a Notice of Preparation (NOP) and Initial Study, which can be accessed at the State Clearinghouse:
The updated WDRs will be grounded in the sediment, temperature, and dissolved oxygen TMDLs adopted by the Regional Board in 2005 (Scott River) and 2006 (Shasta River), which are available at the following links:
These TMDLs were designed to address major water quality impairments caused by sediment runoff, thermal pollution, and oxygen depletion—impacts tied largely to over-irrigation, livestock management, and channel modifications.
Legislative Action: AB 263 Would Extend Emergency Flow Protections
In a major step forward for salmon recovery and water justice, AB 263—a bill introduced by Assemblymember Chris Rogers and sponsored by the Karuk Tribe, Yurok Tribe, and California Coastkeeper Alliance —was passed on April 9, 2025, out of the California Assembly Committee on Water, Parks, and Wildlife. The bill would maintain emergency flow regulations on the Scott and Shasta Rivers while the State Water Board works to establish permanent instream flow standards. This legislation responds to ongoing threats to endangered salmon from excessive diversions and groundwater pumping—threats that persist even as drought declarations expire.
Supporters of the bill emphasize that without continued flow protections, recent progress—such as the Klamath River dam removals—could be undermined. The bill is seen as a critical bridge between short-term emergency action and the long-term regulatory process already underway. As Karuk Tribe Vice Chairman Kenneth Brink stated, “AB 263 helps maintain the momentum of the Klamath River restoration so that salmon have a home to come back to and spawn.”
Why This Matters
The Scott and Shasta Rivers are at a breaking point, but the public processes taking place right now present a unique opportunity for recovery. The combination of emergency flows, enforceable pollution limits through WDRs, and sustainable water planning offers the most comprehensive opportunity in decades to reverse the decline of salmon populations and protect Tribal and public trust resources.
EPIC will continue to track these processes closely and we plan to submit formal comments to advocate for a science-based, equity-centered water policy that puts the health of rivers and communities first. Stay tuned for updates on public hearings, comment deadlines, and advocacy tools.
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