Allocating a Share of San Joaquin River Water to the Environment Shows Promise

Source: California Department of Water Resources

Source: California Department of Water Resources

By Jeffrey Mount, Brian Gray, Ellen Hanak, PPIC Water Policy Center, Peter Moyle, UC Davis Center for Watershed Sciences


In September 2016, the State Water Board released its draft plan for new environmental flow requirements in the San Joaquin River watershed. The board’s proposal contains a novel—and controversial—recommendation. Instead of following the traditional approach of setting minimum flows to meet specific environmental needs at specific times of the year, the board proposes to allocate a block of water each year to improve habitat for fish and wildlife in the lower San Joaquin River and its tributaries—the Stanislaus, Tuolumne, and Merced.

As we have argued in several recent reports, assigning a block of water to the environment has numerous advantages over the traditional regulatory approach. Done well, it could improve ecosystem performance and the efficiency of environmental water use, while reducing uncertainty for other water users.

Here we outline the essence of the board’s proposal and describe its strengths and areas for improvement. We conclude with some suggestions for how these ideas could be incorporated fruitfully into settlement negotiations with stakeholders in the watershed.

The board’s proposal: Allocating a share of water for the environment

Native fishes in the Lower San Joaquin River and its tributaries—particularly salmon and steelhead—have been declining for decades. The board has authority to address this decline by setting flow requirements to protect beneficial uses of California’s waters. This authority derives from a variety of California laws that are not dependent on either the federal Clean Water Act or the Endangered Species Act.

For fish, the board traditionally sets minimum flow standards tailored to meet the requirements of specific life stages of each of the protected species (e.g., pulse flows to facilitate migration up and down the river, cold water for eggs and young fish). These flows are made available through a combination of releases from reservoirs and limitations on diversions by other water users.

The proposed new approach is to allocate a portion of the February-through-June “unimpaired flow” on the Stanislaus, Tuolumne, and Merced tributaries to native fish. Unimpaired flow is the volume of water that would be present in the tributaries without reservoirs or diversions.

The plan proposes that an average of 40% of this flow—with a range of 30-50%—be assigned to meet environmental objectives. We have no position on the merits of this proposed share, which is likely to be a matter for negotiation on each tributary.

More important is the flexible way that environmental managers could use this water. Under the proposal, they could shift flows as needed for different hydrologic conditions or locations to meet biological goals for protected species. This could include storing water for pulse flow releases—such as to improve water quality or provide migration cues for fish—and holding water until late summer to bolster cold water releases from reservoirs.

Why this approach is a good idea

The board’s proposal to allocate a flexibly managed block of water to the environment is an improvement over the traditional setting of minimum flow standards in three ways:

  • Efficiency: The block approach allows for better use of environmental water to benefit fish. Managers can more easily adapt to changing conditions such as droughts and floods, time flow releases for maximum effect, vary the way they apply water from year-to-year, and more nimbly respond to new biological and ecological information. This would increase the efficiency of environmental water use while also improving its effectiveness.
  • Predictability: A block of water is simple, transparent, and easier to incorporate into environmental and operations planning.  Assigning a specific quantity of water to environmental uses would give more certainty to other water users, because they would know the percentage of unimpaired flow available to them.
  • Shared responsibility: Allocating a flexibly managed block of water to environmental uses would ensure that the environment is better integrated into the water rights system. Environmental water managers would have a seat at the table in water management, deciding how best to use their allocation just as other water users do, and the environmental water block would share equally in abundance and shortage along with other beneficial uses.

What would make this approach even better

In addition to this novel approach to establishing flow standards, the draft plan encourages stakeholders and interested parties to negotiate settlements that they would submit to the board for approval. Such negotiations are a good way to harness local knowledge, creativity, and cooperation.

We recommend that negotiators and the board retain the idea of allocating a block of water to the environment and consider several improvements:

  • Allow carryover: The draft plan requires that all environmental water be used in the same water year. To enhance efficiency and to hedge against drought, it should be possible to store some environmental water in surface reservoirs or groundwater basins (with rules to avoid impacts to other users). A good example of the benefits of integrating groundwater and surface water storage with environmental flow management comes from the Yuba River watershed in northern California.
  • Allow trading: Environmental water efficiency also would be enhanced if the plan explicitly allowed the buying and selling of this water. A good example comes from Australia, where environmental managers regularly lease some of their water to fine-tune flow management in different catchments. Some revenues from leasing are also used to support ecosystem investments.
  • Encourage augmentation: The existence of a well-managed environmental water budget would present an opportunity for better employing conserved urban and agricultural water for environmental purposes. Allowing the budget to be easily augmented with water acquired on a permanent, long-term, or temporary basis through voluntary purchases or donations would increase resources for environmental management.
  • Assign responsibility: The proposed governance structure for environmental water management is a large, multi-party committee of regulatory and planning agencies, project operators, water users, and other stakeholders (Draft Plan, Appendix K, page 32). This structure is cumbersome and lacks the independence and flexibility needed to administer the block of water in a timely fashion. The revised plan should create an environmental water manager—perhaps similar to the environmental water holder in Victoria, Australia—with authority and staffing to administer the environmental water for defined biological objectives.
  • Improve planning: The long-range biological goals and objectives—beyond improving salmonid populations—are not well articulated in the current plan. Management of the Stanislaus, Tuolumne, and Merced tributaries needs an overarching biodiversity plan that takes a broader, ecosystem-based approach and defines how the environmental water allocation would benefit salmonids as well as other riverine, riparian, and wetland species. The plan should achieve multiple environmental benefits from the water, focusing on different priorities in different types of water years. Such a plan could be developed relatively quickly, based on available scientific information and with input from stakeholders. The biodiversity plan should be revised every 7-10 years, based on improvements in scientific understanding of ecosystem performance. Victoria, Australia provides a model for developing pragmatic, ecosystem-based plans to maximize the benefits of environmental water.
  • Monitor and Adapt: It is critical that management of the environmental water allocation be supported by a robust, transparent, and science-based monitoring program. This program should report to the environmental water manager, who would use the information to guide annual allocation and use decisions, adaptation and management experimentation, and long-term planning and evaluation.  Funding this effort may require pooling of resources among agencies and water users.


The board’s proposal to use a percentage of unimpaired flow as an environmental standard and budget for the Stanislaus, Tuolumne, and Merced tributaries has generated a great deal of controversy in the water-user community. While this is understandable, we encourage all interested parties to carefully examine the merits of this approach and to consider its compensating advantages. Block allocations of environmental water—flexibly managed and supported by science, sound governance, and planning—can be an effective tool for achieving the twin goals of ecosystem protection and water supply reliability.  Negotiating settlements that seek to achieve multiple benefits from blocks of environmental flows is a promising direction for using California’s water more efficiently and effectively.

Further Reading

California State Water Resources Control Board. 2016. Draft Revised Substitute Environmental Document in Support of Potential Changes to the Water Quality Control Plan for the Bay-Delta: San Joaquin River Flows and Southern Delta Water Quality.

Escriva-Bou, A., H. McCann, E. Hanak, J. Lund, and B. Gray.  2016. Accounting for California’s Water. Public Policy Institute of California.

Gray, B., E. Hanak, R. Frank, R. Howitt, J. Lund, L. Szeptycki, and B. Thompson.   2015. Allocating California’s Water: Directions for Reform. Public Policy Institute of California.

Lund, J., E. Hanak, B. Thompson, B. Gray, J. Mount, K. Jessoe. 2014. Why give away fish flows for free during drought? California Waterblog.

Lund, J. 2015. Urban water conservation for birds.  California Waterblog.

Mount, J., B. Gray, C. Chappelle, J. Doolan, T. Grantham and N. Seavy. 2016. Managing Water for the Environment During Drought: Lessons from Victoria, Australia. Public Policy Institute of California.

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7 Responses to Allocating a Share of San Joaquin River Water to the Environment Shows Promise

  1. Frances Griffin says:

    Long overdue!


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  4. Gordon M. Armstrong says:

    While this solution does address many concerns and allows for much needed flexibility it does not include consideration of current river level. The fish flow releases (on the Stanislaus River) do not take into account the current flow or level. The concern is releases on the Stanislaus that occur when the San Joaquin River is low. This results in an abnormal high flow condition on the Stanislaus which impacts the river channel adversely. Normally when the level is high on the Stanislaus the level is high on the San Joaquin, which greatly reduces the flow rate on the lower Stanislaus. Releases on the Stanislaus when the San Joaquin is low results in greatly increased sand and solids flow on the Stanislaus. I live alongside the lower Stanislaus and see the results of the abnormally high flow rate for extended periods: It is very detrimental to fish and wildlife. Up until the fish releases started there was a bait clam harvesting business on the Stanislaus. There were clams up to 2in in size. Now the largest are 1/2″ or less. The sand bars the clams existed in have been washed away and the sand deposited in the San Joaquin River channel.


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  6. Sari Sommarstrom says:

    With your comparison to Victoria, Australia’s program, one critical part of theirs appears missing in your recommendations: financial compensation for the lost/reallocated water rights. Water users for irrigation and municipal uses have become dependent upon these current water rights. Greater efficiencies can reduce some of the original and current water needs, but economic factors are involved that appear to be ignored by SWRCB’s proposal. Yes, environmental flows should have been incorporated before appropriative rights were allocated, back when. But now the State needs to be reasonable in how it turns back the clock to better instream flows. Compensation would be fair. Victoria got it right; California has not.


  7. San Joaquin River runs dry, the dry section should be excavated and deepened. This is like dredging water ways for ships. The sediment needs to be remove and rivers need to be deepened with deep water holes along the rivers path for fish to congregate and help the water stay cooler.


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