Resurrecting the Delta for Desirable Fishes

by Peter Moyle, Carson Jeffres, John Durand

Cache Slough sunrise. Photo by Matt Young

The Delta is described in many ways.  When extolling the Delta as a tourist destination, it is described as a place of bucolic beauty; islands of productive farmland are threaded by meandering channels of sparkling water, a place to boat, fish, view wildlife, and grow cherries and pears.

But when its future is discussed, especially in relation to big water projects, this heavenly place is often portrayed as being on its way to an aquatic Hellscape.

The Sacramento Bee recently (April 8, 2008) published a reasonable editorial advocating a holistic approach to solving Delta problems.  But the editors chose language to describe the Delta such as:  it is “dying as the planet warms” and it is on the verge of “ecosystem collapse.” This language tracks that of groups that want to “save the Delta,” especially from proposed changes to its human-dominated plumbing system.

At the risk being labeled heretics, we say the Delta is not dying, and its ecosystem is not on the verge of collapse, but that it is changing.

The last time California faced real collapse of aquatic ecosystems was before the passage of the state and federal clean water acts in the 1970s, which eliminated or greatly reduced the dumping of huge volumes of toxic material into the estuary.  The present Delta, as measured by total fish populations, species diversity, navigability, migratory waterfowl abundance, and other measures, even water quality, is a ‘healthy’ ecosystem in many ways.

The most likely future Delta, even after widespread levee failure, will not feature a collapsed ecosystem (whatever that may be) or even a particularly unhealthy Delta ecosystem.  No matter what happens, there will still be fish and fisheries in the Delta, as well as boating, abundant wildlife, complex food webs and prosperous farms. But the future ecosystem may not have many of the species we find desirable today, especially endangered species such as delta smelt and winter-run Chinook salmon. Current land use patterns are also likely to change, away from urbanization and low-value agriculture.

If present trends continue, native fishes in the Delta will be replaced largely by alien species such as wakasagi smelt, Mississippi silversides, and largemouth bass. Deeply  subsided islands will be transformed via levee collapses to large open areas of tidal brackish water. These habitats will favor salt-tolerant species such as striped bass, starry flounder, crangon shrimp, splittail and various species of Japanese gobies.  In short, at least in the water, the fishes tell us that, no matter what happens, there will be thriving novel ecosystems that will support many of the same functions as today. The present ecosystem is already quite different from earlier manifestations of the ecosystem, especially the original historic ecosystem. Native species disappear while non-native species increase.

But we don’t have to accept whatever Delta ecosystem comes our way. To some extent, we can choose the species making up the future Delta ecosystem as well as many of its physical features, if we make some tough management decisions and accept that ecosystem changes will continue, some beyond our control.  Today’s somewhat foggy general vision of the Delta’s future seems to be that it will remain in its present configuration forever, with levees and channels maintained despite continual land subsidence, bigger storms, higher tides, and changing habitats and economies.  This Delta is assumed to continue as a freshwater system, thanks to large pulses of water from dams.  Despite these pulses, native fishes will gradually disappear, although fall-run Chinook salmon runs may continue due to hatcheries and trucking operations.  Delta smelt and longfin smelt will likely be extinct; they will no longer drive water decisions unless maintained by artificial propagation, like salmon. Fisheries for largemouth bass and other warm-water fishes will expand, dominating the system even more than today.

This vision does not have to prevail in all of the Delta.  We recently wrote a report that provides an alternative vision (Moyle et al. 2018, Making the Delta a Better Place for Native Fishes (   The vision we present is a modified version of some earlier thoughts (Moyle et al. 2013, and other references listed below).  The key to this vision is that management for native species and related values focuses on the North Delta Arc, a string of habitats connected by the Sacramento River.  The  Arc starts in the Yolo Bypass, continues through the Cache Slough region, then down the river past Rio Vista and into Suisun Marsh.  It also includes the Cosumnes-Mokelumne river corridor, to the Sacramento River.

Under this vision, the central and south Delta are treated as habitat that is, in fact, inhospitable for native fishes.  Indeed, native fishes may need to be excluded from these parts of the Delta, especially in summer.  The main issue for the central and south Delta is creation of a corridor for safe passage of adult and juvenile salmon and steelhead between San Francisco Bay and the San Joaquin, Tuolumne, Merced, and Stanislaus rivers.  This division of the Delta into two ecosystems is tacitly recognized already by most restoration projects (e.g., EcoRestore) as being located in the Arc.  This area provides the best opportunities because of habitat diversity and the fact that the Sacramento River connects these diverse habitats. The river also serves as the major migration corridor for fishes.

Our paper recommends 17 actions, listed below. Collectively, these actions could significantly improve habitat for native fishes, either directly or indirectly through stressor reduction and through development of new approaches via research. They at least will slow the ecosystem shift now occurring in favor of native species, floodplains, and wetlands.


  1. Four Easy Fixes (Fremont Weir, McCormick –Williams Tract, Delta smelt beaches, Putah Creek restoration).
  2. Expand Monitoring for Estuarine Health
  3. Provide a Water Right for the Environment
  4. Develop a Functional Flow Regime for the Delta
  5. Expedite Permitting and Implementation of Habitat Restoration Projects


  1. Expand EcoRestore and Learn from First 30,000 Acres
  2. Expand Restoration Projects in the North Delta Habitat Arc
  3. Establish Suisun Marsh as a Horizontal Levee
  4. Eliminate Predation Problems at Clifton Court Forebay
  5. Improve Delta Passage for Juvenile Salmon from the San Joaquin River and Tributaries.


  1. Reversing Subsidence in the Delta
  2. Accommodating Climate Change
  3. Reducing Impacts of Invasive species
  4. Reducing Impacts of Pesticides, Micro-contaminants, and Other Toxic Materials


  1. Experimenting with Island Flooding
  2. Evaluating Restoration Projects
  3. Developing a Stable Source of Innovative Research Funding.

As the report states: “The alternative to taking these and other actions is to continue on our present path, which is leading to the extinction of native fishes and the loss of significant fisheries for Chinook salmon, steelhead, striped bass and other fishes. It is important to remember that the Delta will always support a complex ecosystem. But whether that ecosystem is one that is desirable and consistent with our needs is up to us.”

The vision expressed by our report accepts that changes to the Delta ecosystem are inevitable but that, optimistically, we can collectively direct some of the change towards a more desirable state than will exist without high levels of additional activity. This vision can encompass actions favored by those who want to “save” the Delta, as well as those who envision a managed ecosystem that includes most of the remaining native fish fauna, as well as many other desirable elements, native and non-native.  It is not a vision that supports the rhetoric of a dying Delta or the Delta as a collapsed ecosystem, a rhetoric which does not lead to plausible actions to improve reality.

Peter B. Moyle is a UC Davis Professor Emeritus of fish biology and an associate director of the Center for Watershed Sciences. John Durand is a researcher specializing in estuarine ecology and restoration at the Center for Watershed Sciences.  Carson Jeffres is a researcher specializing in fish ecology at the Center for Watershed Sciences.

Further reading

Durand, J., P. Moyle, and A. Manfree. 2017. Reconciling conservation and human use in the Delta. UCD California Water Blog, February 12, 2017.

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. San Francisco: Public Policy Institute of California. Available at

Hobbs, J.A, P.B. Moyle, N. Fangue and R. E. Connon. 2017. Is extinction inevitable for Delta Smelt and Longfin Smelt? An opinion and recommendations for recovery.  San Francisco Estuary and Watershed Science 15 (2):  San Francisco Estuary and Watershed Science 15(2). jmie_sfews_35759. Retrieved from:

Lund, J., E. Hanak, W. Fleenor, W. Bennett, R. Howitt, J. Mount, and P. B. Moyle.  2010. Comparing futures for the Sacramento-San Joaquin Delta. Berkeley University of California Press. 230 pp.

Moyle. P.B. W. Bennett, J. Durand, W. Fleenor, J. Lund, J. Mount, E. Hanak, and B. Gray. 2012. Reconciling wild things with tamed species- a future for native fish species in the Delta. California Water Blog. Center for Watershed Sciences, June 15, 2012.

Moyle, P. B., W. Bennett, J. Durand, W. Fleenor, B. Gray, E. Hanak, J. Lund, J. Mount. 2012. Where the wild things aren’t: making the Delta a better place for native species. San Francisco: Public Policy Institute of California. 53 pages.

Moyle, P. B., W. A. Bennett, W. E. Fleenor, and Jay R. Lund. 2010. Habitat variability and complexity in the upper San Francisco Estuary. San Francisco Estuary and Watershed Science  8(3): 1-24.

 Moyle, P., J. Durand, A. Manfree. 2016. The North Delta habitat arc: an ecosystem strategy for saving fish. UCD Center for Watershed Sciences California WaterBlog. November 6. 2016.

Moyle, P.B., J. A. Hobbs, and J. R. Durand. 2018.  Delta smelt and the politics of water in California.  Fisheries 43:42-51.

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

Moyle, P.B., C. Jeffres, and J. Durand. 2018, Making the Delta a Better Place for Native Fishes (

Opperman, J.J, P.B. Moyle, E.W. Larsen, J.L. Florsheim, and A.D. Manfree. 2017 Floodplains: Processes, Ecosystems, and Services in Temperate Regions. Berkeley: University of California Press.


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10 Responses to Resurrecting the Delta for Desirable Fishes

  1. J Rizzi says:

    1 1/2 mile replacement of levee with 1.5 mile fish screen keeps all life in Delta and out of Clifton Court Forebay (deals with #9 &10 in article) but it also allows water exporters to export water without KILLING any fish.

    Benicia bridge 1/12 open, 1/12 shipping lock and 10/12 tidally controlled lovers to reduce salt water intrusion, there by making the Delta more of a fresh water Delta without adding more fresh water flows. Win Win for all. (NEVER considered in past, but similar option have been) for more details.

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  3. Richard S. says:

    You always have the possibilities of entrainment and impingement when using screens.

    • Joseph Rizzi says:

      Wrong. . Entrainment & impingement is due to water speed over screen. 1,500,000 square feet of upscreen will create slow enough water speed over screens that are 1/3 smaller than recommended. Alternative is use ultra filters like ZeeWeed.

  4. Jan says:

    You started the article with: “When extolling the Delta as a tourist destination, it is described as a place of bucolic beauty; islands of productive farmland are threaded by meandering channels of sparkling water, a place to boat, fish, view wildlife, and grow cherries and pears.” Do you understand what that means and what is at risk with the Delta Tunnel project (Cal WaterFix)? Because the project is planned to go through the heart of that place of bucolic beauty, it will unnecessarily take away the ability for visitors and residents to go to and enjoy that favorite place.

    The latest testimonies to the Water Board Hearings on April 20 and 23 from Delta boating experts clearly point out that this project, due to the massive amounts of barge traffic (at least 9400 barge trips), massive amounts of pile driving (over 23,000 piles with over 10,000,000 strikes from giant pile driving rigs), massive amounts of traffic on two lane Delta roadways (both from endless columns of construction trucks coupled with bridge openings on commuter highways like Hwy 4 which currently never open), massive influxes of construction workers, massive amounts of tunnel muck dumped on Delta islands (30,000,000 cubic yards), will cause a commensurate massive negative impact on Delta recreation.

    So it is nice that you stated that, but Peter Moyle is an advocate for the Delta Tunnels. It’s quite disappointing.

  5. Jan says:

    Everyone knows that the #1 problem in the Delta affecting fish is the reduction of fresh water flows due to over-exporting. Moving the pumps, while it will reduce the reverse flows down Middle River south and reduce entrapment now caused by the old fish screen technology, it doesn’t solve the real problem. In fact, real scientists agree (Bay Institute in the Delta Flow Requirements reports, Independent Science Board, NOAA Scientists, independent Delta scientists, etc.) that the main issue for fish in the Delta is lack of fresh water flows. But state scientists are all told that the amount to be exported is mandated and their efforts need to be to find other ways to save fish without reducing flows. The Legislature in 2009 mandated reducing exports to meet the Delta Flow requirements. Your 17 “improvements” are nice – but the main improvement needed is reduced exports. So what problem will that cause? Central Valley farmers need to reduce the never-ending expansion of almond orchard acreage to balance the need with available water.

    The problem is that this article ignores the elephant in the room – over-exporting. Step back and look at the big picture and seek different alternatives than taking more and more water out of the Delta. Include a real analysis of data flow requirements.

    • J Rizzi says:

      I am not for tunnels. But I see limiting the salt water inflow at Benicia bridge will make the Delta a large fresh water Delta. 3 steps 1/12 under the bridge (north side) kept open for fish, small water craft, nature, 1/12 add shipping lock to protect bridges and ships as well as stop salt intrusion, 10/12 put in tidally controlled louvers (like a dryer vent) that opens and lets fresh water out but closes with the incoming tide to keep most of the salt water out. As for Clifton Court Forebay, it should only be filled at night and closed during the day.

      • Jan says:

        I thought that option (or one similar) was studied and determined not to be feasible due to the depth of the channel, restrictions on all of the barges and tankers that come up and down (they didn’t want to make them go through a lock for fear of Stockton losing too much business), and species that need a mix of fresh and salt water habitat like the Delta smelt. But I’m no expert on that so if it is feasible, I wonder why it isn’t looked at. Perhaps with global warming and salt water already as far inland as Franks Tract there isn’t enough fresh water? I wonder how high the wall would need to be.

      • J Rizzi says:

        The study was for a DAM with a lock. I am opposed to a DAM because of environmental issues. That is why I start with keeping 1/12 of the channel open. Currently, per tug boat people, Benicia Bridge is a hazard today with the currents, bridge supports and curve under bridges, so a shipping lock would be helpful and add needed safety. Added time, if any, would be minimal for shipping traffic. Like you, water people, think that this has already been studied, so it is discounted out of hand. FYI … the wall height should be 5 to 10 feet over high tide level. Shipping channel is dredged to 50 deep. With one section open and only having louvers there will be salt water intrusion but it should not reach the Antioch bridge. If you want a more detailed description I can send you a flyer (

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