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State Water Resources Control Board Releases Final Scientific Basis Report for Phase II Update of the Bay-Delta Plan

The State Water Resources Control Board (SWRCB) is updating the Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (Bay-Delta Plan). Currently, the SWRCB is conducting two phases of the update process. Phase I has focused on flow requirements in the San Joaquin River watershed. Phase II of the process focuses on requirements for instream flows and cold water habitat in the Sacramento River watershed.

On October 4, 2017, the SWRCB posted a “Notice Regarding Information and Future Updates on the Phase II Update of the Bay-Delta Plan” (Phase II Notice) on its website. The SWRCB also posted the final Scientific Basis Report in support of the Phase II of the Bay-Delta Plan Update (Phase II), an updated version of the Sacramento Water Allocation Model, and a fact sheet for the Phase II Update (Fact Sheet) on the same day.



The Bay-Delta Plan, issued by the SWRCB pursuant to its authority under the federal Clean Water Act and state Porter-Cologne Water Quality Control Act, identifies beneficial uses of water in the Bay-Delta, water quality objectives to reasonably protect those uses, and a program of implementation to achieve the objectives. The current Bay-Delta Plan requirements were established in 1995 and were last updated in 2006 with minor modifications. The Scientific Basis Report was prepared by staff and consultants of the SWRCB to support Phase II and will ultimately be included in a larger Staff Report that will address information on environmental, economic, and other analyses of potential changes to the Bay-Delta Plan. Although the Scientific Basis Report acknowledges that many issues have caused the decline of native fish species, the objectives proposed for the Phase II Update of the Bay-Delta Plan focus exclusively on flow and water quality requirements because the SWRCB believes that those issues are within the jurisdiction and responsibility of the SWRCB. (Scientific Basis Report at 1-2.) The Report explains, echoing statements from the existing program of implementation, that coordination and collaboration with other efforts in the Bay-Delta will complement the SWRCB’s water quality control planning and implementation. (Id. at 1-14)


Key Elements of the Proposed Phase II Update

The Phase II Notice describes four main elements of the Phase II Update: 1) tributary inflow requirements; 2) Delta outflow requirements; 3) interior Delta flow requirements; and 4) cold water habitat requirements. (Phase II Notice at 1.) The first three proposed elements would include both narrative and numeric objectives, while the proposed cold water habitat requirements would contain narrative objectives only. (Scientific Basis Report at 1-18 – 1-23.)

The Scientific Basis Report proposes tributary inflow requirements between 35-75% of unimpaired flows. (Scientific Basis Report at 1-19.) Proposed numeric objectives for outflow requirements would maintain existing flow requirements in Table 3 of the current Bay-Delta Plan, but would replace Table 4 of the current plan with “Inflow-based Delta outflow objectives.” (Id. at 1-21)

In addition, the Scientific Basis Report’s proposed cold water habitat requirements will attempt to ensure that reservoir releases are sufficiently cool to protect salmon species in the Sacramento River watershed. (Id. at 1-22.) The narrative objective recommended by the Report will also propose alternate measures, such as passage above dams, which may protect salmon from temperature impacts. (Id. at 1-22.) The cold water habitat requirements are not intended to contain numeric objectives because optimal temperatures may vary depending on the nature of each tributary, the fish within them, and the potential availability of other actions to address cold water habitat concerns. (Id.)

The Report contemplates that adaptive management will be an important component of implementing the updated Bay-Delta Plan. (Id. at 1-15 – 1-16.) Adaptive management will involve shifting and sculpting flows to achieve specific biological objectives. (Id. at 1-16.) It will also allow for experiments with different flow regimes. (See id.)


Voluntary Agreements

The Scientific Basis Report explicitly acknowledges that voluntary agreements among Sacramento River stakeholders can help achieve the biological goals that will ultimately drive the updated Bay-Delta Plan. (Id. at 5-48.) Indeed, the Scientific Basis Report explicitly endorses stakeholder collaboration to reach “early voluntary agreements that may also help inform and accelerate Bay-Delta planning” itself. (Id. at 5-48 – 5-49.) All voluntary agreements intended to implement the updated Bay-Delta Plan will be subject to acceptance by the SWRCB. (Id. at 5-49.)


Conclusion and Implications

The Phase II Update will have implications for water users throughout the state. The next step in the Phase II process will be the preparation of a substitute environmental document that will analyze various alternatives for the Phase II Update, including SWRCB staff’s recommendations in the Scientific Basis Report. Additional information regarding the Phase II process is available on the SWRCB’s website:

(Sam Bivins, Meredith Nikkel)