Advice on Voluntary Settlements for California’s Bay-Delta Water Quality Control Plan Part 2: Recommended Actions to Improve Ecological Function in the Delta

by Jeffrey Mount, PPIC Water Policy Center*

The Sacramento-San Joaquin Delta.


By strategically linking freshwater flow releases with the management of tidal energy and investments in landscape changes in the Delta, it is possible to improve ecological food webs and habitat for native species and reduce the effects of pollutants. Projects to address these problems should be concentrated in the North Delta and Suisun Marsh, and can be completed within 15 years. These include habitat improvements on flood bypasses, terminal channels, shallow open-water habitat, river-tide transition zones, and tidal marshlands, along with strategies for reducing harmful algal blooms. This integrated, ecosystem-based approach—in which freshwater flows, tides, and landscapes are managed together—is preferable to current approaches that manage them mostly in isolation from one another, and for a few species of fish.


The State Water Board is preparing a new Bay-Delta Water Quality Control Plan. Parties affected by this plan are attempting to negotiate voluntary settlement agreements for the Board to consider. A group of us—experts on the Delta and not part of any negotiations or representing any interested parties*—have come up with a series of recommendations to help inform these negotiations. This is the second in a series of three blog posts that reflect our discussions and conclusions. In our previous post, we recommended that negotiating parties and the Board identify and focus on a set of ecological goals for the Sacramento-San Joaquin Delta that could be achieved over the next 15 years. That post also lays out our view of the problems facing the Delta and the tools that can be used to better manage it.  Here we recommend near-term actions with the greatest likelihood of achieving significant and measurable progress in improving ecosystem conditions.

These recommendations are based principally on the professional judgment of the group, guided by a set of constraints on Delta management that will need to be taken into account (see text box). Many of the actions will be familiar to those working on ecosystem issues in the Delta.

Management Options to Improve Delta Ecosystem Conditions

The Delta and its watershed face many different environmental problems, and multiple tools are available to address them. There are three general management options (all include a commitment to improve water quality through management of pollutants):

  1. Focus on flow volumes: Emphasize allocation of freshwater flows to the ecosystem, with significant increases in outflow from the Delta into San Francisco Bay and the ocean.
  2. Focus on landscape management: Improve habitat through landscape management with no major changes in the current allocation of freshwater flows.
  3. Use a portfolio of actions: Increase flexibility in the timing and magnitude of freshwater flows and link these to landscape modifications that increase habitat benefits and take advantage of tidal energy (described below).

All three approaches have scientific merits and uncertainties; they also present different social and economic trade-offs. The first—significant increases in Delta outflows—is based on the historical connection between cool, wet years and improved population counts of some species, including pelagic fishes. This relationship is no longer as clear, however, particularly for Delta smelt (see the text box). To fully test this approach the Board would have to re-allocate very large amounts of water to outflow, because modest, incremental changes in outflow are unlikely to result in substantial changes in Delta conditions.  This would have large impacts on available water supplies.

The second approach—relying principally on landscape changes to improve conditions—seeks to reverse some of the extensive losses in habitat caused by land reclamation, channelization, and flood control projects.  Like the high outflow approach, this too has merit. But it ignores the importance of flow timing and magnitude to ecosystem functions and the life-history requirements of desirable plants and animals.

In our view, the third option—a portfolio that includes increased flexibility in how flows are managed, improvements in landscapes, and management of tides—has the highest likelihood of substantially improving ecosystem conditions. This approach also has the best chance of improving our understanding of how to manage the Delta in the future. To be effective, this option will involve reconnecting significant, contiguous areas of land—some currently held in private ownership—to freshwater flows and tides. This will require both the cooperation of Delta landowners and funding to acquire and manage these lands. Changes in flow management could also introduce some new constraints on water availability for human uses. However, by targeting flow releases we expect that this portfolio approach has the potential to use water, land, and financial resources most efficiently to improve ecosystem conditions in the Delta.

We next briefly describe what we mean by management of freshwater flows and tides.  We then outline six project areas for the recommended portfolio approach.

Managing Freshwater Flows

Managing fresh water in conjunction with the landscape and tides will require water users and regulators to shift away from the current approach—which focuses on adhering to minimum instream flow and water quality regulations—toward more flexible management. Flexibility includes allowing for real-time adjustments to hydrologic conditions (for example, to take advantage of pulse flows from storms), experimental flows to test ecological responses to landscape changes, and strategic use of flows to improve water quality. This also involves narrowly targeting flows to improve ecological conditions in specific areas, which increases the efficiency of the use of this water.

Some of us have presented ideas on how to accomplish this using ecosystem water budgets coordinated by designated “ecosystem trustees” (Mount et al. 2017). Regardless of the approach, there is one basic requirement: the ecosystem must have assets to enable managers to adjust the timing of flow releases and diversions. These assets can include a portion of annual flow that can be flexibly used, stored, or traded; water stored in reservoirs or groundwater basins; shares in storage and conveyance capacity; and financial resources to purchase water.

Managing Tides

Tides drive most water movement and mixing in the Delta and the San Francisco estuary. They are vital for connecting nutrients and supporting food webs across tidal marshes and channels, helping to address food limitations within the Delta. The concept of managing tides may be novel to policymakers, but their ecological relevance is grounded in studies showing that ecosystem productivity increases when different habitat types are connected by tidal flows (Cloern 2007).

Tools for managing tides include changing the Delta’s landscape and channels, as well as using gates and barriers. For example, restoring large tracts of tidal marsh will expand the area inundated by tides and dissipate tidal energy, reducing tidal influence elsewhere in the Delta. Gates and barriers can be used to direct tidal flows at the local scale, helping to move food resources (and fish) into or out of specific areas. Landscape changes that do not consider tidal effects can lead to unanticipated or unwanted consequences.

 Six Recommended Flow-Tide-Landscape Projects

To improve food webs, maximize habitat for desirable plants and animals, reduce impacts of algal blooms, and increase understanding of the Delta, we recommend a 15-year commitment to a suite of six linked projects. Five of these projects focus on managing landscapes, tides, and freshwater flows—principally within the North Delta, Suisun Marsh, and the Sacramento River floodplains. The sixth project focuses on building and applying knowledge to reduce the human and environmental health risks of algal blooms.

  • Flood bypasses: Yolo and Sutter Bypasses—the two large flood bypasses on the Sacramento River—have the greatest potential for reestablishing floodplain function in the Central Valley and enriching downstream food webs. Water can be directed through weirs onto floodplains to maximize habitat for migratory fishes (e.g., splittail and juvenile salmon), waterfowl, and wading birds. This requires operable weirs to test and refine management actions, improve ecological outcomes, and allow summer agriculture. This approach also may require pulse flow releases to augment natural flows.
  • Terminal channel systems: The North Delta and Suisun Marsh both have networks of dead-end channels that commonly host abundant native fishes (Moyle et al. 2012, 2014). Tidal mixing within these channels is associated with turbid water—which fish may use to avoid predators—and high food web productivity. In the mixing zone of the Deep Water Ship Channel, for example, Delta smelt and other native fish densities are as high as anywhere in the Delta (Feyrer 2017). Landscape changes and freshwater flow pulses can be used to manage these mixing zones in the North Delta to increase productivity. In Suisun Marsh, the salinity control gates could be used to help meet this objective.
  • Shallow open-water habitat: The Delta has approximately 20 square miles of shallow freshwater habitat, mostly in areas where levee breaches have flooded agricultural lands. Landscape changes may be able to enhance food production in these lake-like areas and transfer it to less productive adjacent channels (Lopez et al 2006). Experiments are needed to test this potential source of productivity.
  • Tidal transition zones: Zones where rivers meet the tides account for a large fraction of juvenile salmon mortality within the Delta (Perry et al. 2018). Seaward of these zones, river flows have little influence on the tides, and correspondingly little impact on mortality. Ongoing research shows that it may be possible to increase juvenile salmon survival in tidal transition zones by restoring marshland and making other landscape changes that reduce the influence of the tides in the North Delta. Strategic, short-duration freshwater flow pulses—coupled with improved channel margin habitat—may also help.
  • Tidal marsh habitat: Marshes, including their networks of branching (“dendritic”) channels, are some of the most productive, high-quality habitats within the Delta and estuary (Moyle et al. 2014).  They also form an important link with upland and wetland areas, promoting the exchange of nutrients and animals essential for this productivity. Creation of new marsh-channel systems is essential and will be most effective in large (1,000+ acre) interconnected areas where they were historically abundant (e.g., in the Cache-Lindsay Slough region and Suisun Marsh; see Robinson et al. 2016). Ongoing research shows that pulses of freshwater flow into Cache Slough have promise for improving habitat and food productivity.
  • Algal blooms: A two-pronged approach is needed to address the problem of harmful algal blooms in the Delta: 1) investigating relationships among flows, water quality, and cyanobacteria blooms; and 2) managing freshwater flows, tides, nutrients, and landscapes to reduce these blooms while promoting productivity for Delta food webs.

Except for the management of harmful algal blooms, all of the projects described above are detailed in some form in numerous state planning and regulatory documents (e.g., Bay-Delta Conservation Plan, Delta Plan, California EcoRestore). The San Francisco Estuary Institute has also produced an excellent summary of opportunities for habitat improvement (Robinson et al. 2016). Our proposed approach emphasizes two overarching recommendations: that priorities be based on geography, and that actions combine—wherever appropriate—the flexible allocation of freshwater flows with the management of tides and landscapes.


Why This Approach Is Better than the Current Path

Federal and state efforts to manage the Delta for ecosystem objectives have been unsuccessful, as indicated by declines in native biodiversity and water quality (Gore et al. 2018). The approach outlined here departs from historical efforts in two ways. First, we propose an integrated approach that considers the complex interaction among tidal and river flows, landscapes, and water quality. Past approaches have failed to consider that the benefits of environmental flows depend on their landscape setting, and that the benefits of landscape changes depend on their hydrologic setting.


Second, we take an ecosystem-based view that includes, but extends beyond, population declines of some native fishes listed under federal and state endangered species laws. The integrated approach seeks to improve Delta ecosystem conditions for a broad range of benefits, including fish and wildlife habitat as well as human uses of the Delta’s lands and water.


In our view, this integrated approach is more likely to achieve positive results and efficient use of resources than the current path. And by focusing on the North Delta and Suisun Marsh, measurable benefits can be achieved within a 15-year time frame. To be successful, however, this approach must be supported by a robust, well-funded, and trusted science program―a subject that will be explored in our next blog post.

*This blog post summarizes some of the ideas generated by an informal group of experts who have met several times to explore concepts for better management of the Delta. Group members include (in alphabetical order): Jon Burau (US Geological Survey [USGS]), Jim Cloern (USGS), John Durand (UC Davis), Greg Gartrell (consulting engineer), Brian Gray (PPIC), Ellen Hanak (PPIC), Carson Jeffres (UC Davis), Wim Kimmerer (San Francisco State University), Jay Lund (UC Davis), Jeffrey Mount (PPIC), and Peter Moyle (UC Davis).

Further Reading:

Cloern, J.E. 2007. “Habitat Connectivity and Ecosystem Productivity: Implications from a Simple Model.” The American Naturalist 169:E21-E33

Gore, J., B. Kennedy, R. Kneib, N. Monsen, J. Van Sickle, D. Tuilos. 2018. Independent Review Panel (IRP) Report for the 2017 Long-term Operations Biological Opinions (LOBO) Biennial Science Review: Report to the Delta Science Program. Delta Stewardship Council and Delta Independent Science Program.

Gray, B., B. Thompson, E. Hanak, J. Lund, and J. Mount. 2013. Integrated Management of Delta Stressors: Institutional and Legal Options, Public Policy Institute of California.

Hanak, E., J. Lund, J. Durand, W. Fleenor, B. Gray, J. Medellín-Azuara, J. Mount, P. Moyle, C. Phillips, and B. Thompson. 2013. Stress Relief: Prescriptions for a Healthier Delta Ecosystem, Public Policy Institute of California.

Lopez, C. B., J. E. Cloern, T. S. Schraga, A. J. Little, L. V. Lucas, J. K. Thompson, and J. R. Burau. 2006. “Ecological Values of Shallow-Water Habitats: Implications for the Restoration of Disturbed ecosystems.” Ecosystems 9:422-440.

Lund, J. and P. Moyle. 2018. Ecological Incentives for Delta Water Exports, January 24.

Mount, J., Gray, B., Chappelle, C., Gartrell, G., Grantham, T., Moyle, P., Seavy, N., Szeptycki, L., Thompson, B. 2017. Managing Freshwater Ecosystems: Lessons from Californias 2012-16 Drought. Public Policy Institute of California.

Moyle, P., W. Bennett, J. Durand, W. Fleenor, B. Gray, E. Hanak, J. Lund, and J. Mount. 2012 Where the Wild Things Aren’t: Making the Delta a Better Place for Native Species, Public Policy Institute of California.

Moyle, P.B., A. D. Manfree, and P. L. Fiedler. 2014. Suisun Marsh: Ecological History and Possible Futures. Berkeley: University of California Press.

Perry, R.W., A.C. Pope, J.G. Romine, P.L. Brandes, J.R. Burau, A.R. Blake, A.J. Ammann and C.J. Michel, Flow-Mediated Effects on Travel Time, Routing, and Survival of Juvenile Chinook Salmon in a Spatially Complex, Tidally Forced River Delta. Canadian Journal of Fisheries and Aquatic Sciences.

Robinson, A., Safran, S., Beagle, J., Grenier, L., Grossinger, R., Spotswood, E., Dusterhoff, S., Richey, A. 2016. A Delta Renewed: A Guide to Science-Based Ecological Restoration in the Sacramento-San Joaquin Delta. Delta Landscapes Project. Prepared for the California Department of Fish and Wildlife and Ecosystem Restoration Program. A Report of SFEI-ASC’s Resilient Landscapes Program. SFEI Contribution No. 799. San Francisco Estuary Institute – Aquatic Science Center.

Weins, J., et al. 2017. “Facilitating Adaptive Management in California’s Sacramento–San Joaquin Delta.” San Francisco Estuary and Watershed Sci. 15.

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6 Responses to Advice on Voluntary Settlements for California’s Bay-Delta Water Quality Control Plan Part 2: Recommended Actions to Improve Ecological Function in the Delta

  1. J Rizzi says:

    What a joke! It sounds like lets give up and give out pet projects.

    Fix the problem of fresh water and flows with leaving 1/12 under benicia bridge un-touched, 1/12 gets a shipping lock for safe passage and 10/12 get tidally controlled louvers that open and let fresh water out and slows the tidal forces of seawater intrusion into the Delta. Win – Win for all!!!

    If you want more fresh water to export, first fix the Clifton Court Fish DEATH trap, but replacing the 1 1/2 mile levee with a 1.5 mile fish screen to keep the fish in the Delta un harmed and you can close the SWP and CVP fish relocation facilities to help pay for it since this facilities would not longer be needed once the CVP and SWP pull from CCF with it’s new fish screens. more details available upon request.

  2. Pingback: Advice on Voluntary Settlements for California’s Bay-Delta Water Quality Control Plan Part 3: Science for Ecosystem Management | California WaterBlog

  3. Pingback: Is Ecosystem-Based Management Legal for the Sacramento-San Joaquin Delta? | California WaterBlog

  4. Pingback: An Alternative Approach to Managing the Delta - Public Policy Institute of California

  5. Chris Gilbert says:

    It says there are 4 responses to the post here but I only see one. Help?

    • fissekis says:

      Reposts are counted as responses – so if another platform posted the blog, it’s marked as a response.

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