Advice on Voluntary Settlements for California’s Bay-Delta Water Quality Control Plan Part 1: Addressing a Manageable Suite of Ecosystem Problems

by Jeffrey Mount, PPIC Water Policy Center


The State Water Resources Control Board and the parties seeking to incorporate voluntary settlement agreements in the Bay-Delta Water Quality Control Plan should identify a specific, tractable set of problems that can be addressed over the next 15 years through this plan. We urge the participants to focus a near-term Delta plan on:

1) increasing food-web productivity in the Delta,

2) maximizing high-quality habitat that favors native plants and animals, and

3) improving water quality through nutrient management.

These efforts should recognize the inadequacies of actions focused on single species recovery, and instead focus on the simultaneous and integrated management of flows, tides, and landscapes to improve overall ecosystem function and condition.


The State Water Resources Control Board is revising its Bay-Delta Water Quality Control Plan. The plan is critical for water management because it prescribes water quality and flow requirements in the Sacramento-San Joaquin River and Delta. The Board is considering incorporating Voluntary Settlement Agreements between affected parties to guide development of its water quality plan.

Members of the Brown administration asked a small group of us to offer views on elements that should be considered in such settlements. Each of us met the following criteria: 1) are not part of the settlement negotiations, 2) do not represent any interested stakeholder, and 3) have expertise in water and ecosystem management in the Delta watershed and the San Francisco Estuary. We have prepared three blog posts that reflect our discussions and conclusions. This is the first in the series.

The Delta Challenge

Balancing the competing interests for water in the Delta and its watershed is one of California’s most vexing water policy challenges. This challenge stems from the high economic value of this water throughout the watershed and to export areas, and the highly disrupted ecological conditions of the rivers, the Delta, and the greater San Francisco Estuary. Management for “co-equal” goals, as required by the Delta Reform Act, involves difficult trade-offs that can never fully satisfy all interests.

While there can be value in seeking to simultaneously address all of the many Delta challenges, we think it is more realistic to identify a smaller, well-defined set of problems that can be addressed in the near term (15 years for purposes of this discussion). This requires identifying a set of linked priority actions that might help address ecosystem problems while providing information about how to better manage the Delta in the future. And because we are uncertain about their effectiveness, any suite of actions must include adequate funding and suitable governance for the science needed to test and refine these actions.

Here we recommend three problem areas to address over the next 15 years, as well as three management tools to use in addressing these problems. Two subsequent posts will recommend priority actions and explore possible funding and governance structures.

Toward a Manageable Set of Delta Problems

The Delta and its watershed have many problems. Some will require decades to address (e.g., adaptation to sea level rise and climate change, and improving storage and conveyance). We recommend that the settlement agreements emphasize problems that can be addressed in the near term and help build foundations for long-term solutions. We focused on three fundamental ecological problems:

  • The Delta has become a low-productivity estuary. Reclamation of the Delta landscape eliminated 98% of its high-productivity wetland habitats, leaving an estuary where growth of fish and invertebrates is limited by a small food supply. Low productivity at the base of food webs constrains our ability to meet biological goals for the Delta (Cloern et al. 2016).
  • Ecosystem conditions favor non-native plants and animals over many native species. Current conditions support novel assemblages of organisms that have no historic analog and are difficult to manage. Many non-native species prey on or compete with desirable native fishes. Invasive clams deplete food web productivity. And non-native aquatic vegetation reduces habitat quality for native species and promotes non-native predatory fish (Brown et al. 2016).
  • Water quality is declining. Degradation of water quality by nutrients, pesticides, and other contaminants is affecting human uses of Delta water for recreation and water supply and likely causing harm to native species. An example is the increasing occurrence of blooms of the toxic cyanobacteria Microcystis (Lehman et al. 2010, Brooks et al. 2012).

For several decades, Delta water management has been driven by efforts to recover several fish species listed under the federal and state Endangered Species Acts. These fishes are no longer reliable indicators of changing ecosystem condition, due to their small population sizes. We recommend that the settlement agreements and the Water Quality Control Plan take an ecosystem-based approach that explicitly recognizes that addressing these three fundamental problems will improve conditions for a wide range of terrestrial, wetland, and aquatic plants and animals—including listed fish species—as well as human uses of Delta water.

Three Tools to Address These Delta Problems

To improve productivity, habitat, and water quality, the Water Quality Control Plan will need to employ a range of tools. These include:

  • Managing freshwater flows. Regulating flows into and out of the Delta has been the primary emphasis of past water management actions, and will continue to be important. The focus has been on setting minimum flow and water quality requirements that result in outflow from the Delta into San Francisco Bay, and on regulating export flows when fishes of concern are likely to be harmed by export pumping (Gartrell et al. 2017). A range of flow attributes will need to be managed to address the three near-term ecological problems discussed above. These include: flow regime (frequency, magnitude, duration, timing), quality (including salinity, nutrients, and toxins), and the geographic application of freshwater flows. Flow management will be more effective in confined regions where existing flows are small, rather than broadly across the entire Delta (Brown et al. 2008). More ecologically-effective flow management will require flexibility to respond to new information and changing climatic and hydrologic conditions (Mount et al. 2017).
  • Managing tides. Water quality and circulation in the estuary is largely driven by tides. For most of the Delta, tidal flows dwarf freshwater inflows, particularly in dry times. Historic management of the Delta has viewed tides as a constraint, rather than an opportunity to improve ecosystem conditions. New approaches must accommodate or harness tidal energy to meet flow, habitat, and water quality objectives. This includes considering how changes in inflows and landscapes in one area may affect tidal energy elsewhere (Enright 2014).
  • Managing landscapes. Although most of the focus on Delta management has been on flows, the historic transformation of the Delta through channelization and reclamation of wetlands has arguably had a greater impact on ecosystems. To use freshwater inflows and manage tidal energy more effectively, alterations of flow must be paired with strategic changes to the landscape. These changes may include reconnecting landscapes to tidal action and flood flows and altering existing channels in ways that improve ecological conditions and water quality (Robinson et al. 2016, Durand 2017).

These three tools—managing freshwater flows, tides, and landscapes—must be applied in concert to address the three near-term problems identified here. Applying any one of these tools without the others substantially reduces the likelihood of success.

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 (SFSU), Jay Lund (UC Davis), Jeffrey Mount (PPIC), and Peter Moyle (UC Davis).

Further Reading:

Brooks, M. L. et al. 2012. Life Histories, Salinity Zones, and Sublethal Contributions of Contaminants to Pelagic Fish Declines Illustrated with a Case Study of San Francisco Estuary, California, USA. Estuaries Coasts 35: 603-621.

Brown, L. R., W. Kimmerer, and R. Brown. 2008. Managing Water to Protect Fish: A Review of California’s Environmental Water Account. Environ. Manage. 43: 357-368.

Brown, L. R., W. Kimmerer, J. L. Conrad, S. Lesmeister, and A. Mueller-Solger. 2016. Food Webs of the Delta, Suisun Bay, and Suisun Marsh: An Update on Current Understanding and Possibilities for Management. San Francisco Estuary Watershed Sci. 14.

Cloern, J. E., A. Robinson, A. Richey, L. Grenier, R. Grossinger, K. E. Boyer, J. Burau, E. A. Canuel, J. F. DeGeorge, J. Z. Drexler, C. Enright, E. R. Howe, R. Kneib, A. Mueller–Solger, R. J. Naiman, J. L. Pinckney, S. M. Safran, D. Schoellhamer, and C. Simenstad. 2016. Primary Production in the Delta: Then and Now. San Francisco Estuary and Watershed Science 14.

Durand, J. 2017. Evaluating the Aquatic Habitat Potential of Flooded Polders in the Sacramento-San Joaquin Delta. San Francisco Estuary and Watershed Sci. 15.

Enright, C. 2014. Physical processes and geomorphic features. Pages 45-64. In Moyle, P.B., A. D. Manfree, and P. L. Fiedler. 2014. Suisun Marsh: Ecological History and Possible Futures. Berkeley: University of California Press.

Gartrell, G., Mount, J., Hanak, E., Gray, B. 2017. A New Approach to Accounting For Environmental Water: Insights from the Sacramento-San Joaquin Delta. Public Policy Institute of California.

Lehman, P. W., S. J. Teh, G. L. Boyer, M. L. Nobriga, E. Bass, and C. Hogle. 2010. Initial Impacts of Microcystis aeruginosa Blooms on the Aquatic Food Web in the San Francisco Estuary. Hydrobiologia 637: 229-248.

Mount, J., Gray, B., Chappelle, C., Gartrell, G., Grantham, T., Moyle, P., Seavy, N., Szeptycki, L., Thompson, B. 2017. Managing Freshwater Ecosystems: Lessons from California’s 2012-16 Drought. Public Policy Institute of California.

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: Richmond, CA.

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

Weston, D. P., D. Chen, and M. J. Lydy. 2015. Stormwater-Related Transport of the Insecticides Bifenthrin, Fipronil, Imidacloprid, and Chlorpyrifos Into a Tidal Wetland, San Francisco Bay, California. Sci. Total Environ. 527: 18-25.

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2 Responses to Advice on Voluntary Settlements for California’s Bay-Delta Water Quality Control Plan Part 1: Addressing a Manageable Suite of Ecosystem Problems

  1. Chris Enright says:

    This is a fine analysis and an important contribution to the Board’s process. The three tools–flows, tides, and landscapes–are spot on. They are each powerful “knobs” that can shift the physical/chemical/biological/ecological state of the Delta rapidly. As you say they must be “applied in concert” to be effective. Yet, the management and science process that makes concerted tool application real is always given short shrift. Each incremental action changes the state of the system (changed currents, stages, transport, residence time etc). Before we understand the new state, we will add new actions or nature will add them for us. We can be certain that dynamic outcomes will surprise us, both delight and vex. No action will stand still long enough to be performance measured as a success or failure because the system will continue to shift on purpose and not on purpose. This is quite ok as long as the concerted application of tools has a strong social-scentific decision support process that can present fully conceived alternative futures to decision makers again and again. The Delta is truly a battleship that we only steer with an outboard motor. We must continuously anticipate the ways actions can play out, and then play out again. The need is clear for a continuous (not ad hoc) process of scientific modeling, data analytics, interdisciplinary hypothesis debate, experiment design, community outreach and skillful decision support.
    Slainte maith,
    Chris Enright


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

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