California WaterFix and Delta Smelt

by Peter Moyle and James Hobbs

Frank’s Tract, May 22, 2009. Large expanses of open water are likely to increase in the Delta, providing a justification for WaterFix. Photo by Peter Moyle

The delta smelt is on a trajectory towards extinction in the wild.  Heading into 2017, the spawning adult population was at an all-time low although this past wet winter has apparently seen a small resurgence.  However, increasingly warm summer temperatures in the Delta may dampen any upswing.  Given the long-term trajectory of the population and climate predictions for California, maintaining Delta smelt in the Delta for the next 20-30 years is not likely to happen without significant improvements to the habitat.

So, what happens to the remaining smelt when they encounter California WaterFix? This is the proposal centered around building two tunnels under the Delta to move Sacramento River water directly to the export pumps in the South Delta, benefiting Bay Area and southern California cities and southern Central Valley farms, as well as reducing the problem with reverse flows across the Delta.

In Hobbs et al. (2017) we gave cautious support to WaterFix. In this blog we discuss our reasoning for qualified support for such a controversial large-scale infrastructure project that will affect Delta fish and fisheries.  Our motivation comes from two facts:

(1) The status quo is not sustainable; managing the Delta to optimize freshwater exports for agricultural and urban use while minimizing entrainment of delta smelt in diversions has not been an effective policy for either water users or fish.

(2) Delta infrastructure (mostly levees) is old and increasingly vulnerable to catastrophic failure. Large-scale collapse of Delta levees will likely result in massive intrusion of salt water into Delta, shutting down water exports from the South Delta. Flushing this salty water will require large amounts of fresh water, further stressing water supplies.   The most likely fix will be construction of an emergency freshwater transfer system, which may actually make conditions worse than the status quo, from an ecosystem perspective.

So where do we see reasons to be optimistic about WaterFix from a fish perspective?

  • Entrainment of smelt into the export pumps in the south Delta should be reduced because intakes for the tunnels would be upstream current habitat for delta smelt and would be screened if smelt should occur there.
  • Flows should be managed to reduce the North-South cross-Delta movement of water to create a more East-West estuarine-like gradient of habitat, especially in the north Delta.
  • Large investments should be made in habitat restoration projects (EcoRestore) to benefit native fishes, including delta smelt.


There are huge uncertainties associated with WaterFix and EcoRestore, especially in terms of their effects on fishes.  Together, they are a giant experiment that may or may not work as promised, no matter what the models and experts say.  The giant fish screens for WaterFix, for example, will be pushing screening technology to the limit, having to protect weak swimmers like smelt and small sturgeon, as well as juvenile salmon.

WaterFix is supposed to operate using an adaptive management framework, to deal with uncertainty.  This means management activities can change as construction and operations proceed, as conditions change, and as new information becomes available. The framework for adaptive management is just being established by the Delta Stewardship Council for EcoRestore; it appears to involve many diverse agencies and it isn’t clear how consensus decisions will be achieved.  ‘True’ adaptive management treats each management action as an experiment with testable hypotheses and continuous monitoring that allows success or failure to be determined.  Large-scale experimentation with projects of this magnitude is difficult, even with adequate monitoring.  In short, adaptive management is a good idea but making it work at this scale would be unprecedented.

EcoRestore has many uncertainties as well.  Although restoration of tidal marshes should benefit salmon, water birds, and many other species, the potential for restored tidal wetlands to support delta smelt and other pelagic fishes is at best weakly supported with current scientific data.  Large-scale experimentation with EcoRestore projects will be challenging and will likely require 20+ years of data to make reasonable assessments

There are also trust issues with WaterFix. For it to work as promised, we have to accept that

  • Water will continue to be exported at roughly the same rates as it has been, with no increase in exports, but no decrease as well.
  • It will be operated without significant increases in water being diverted upstream of the Delta.
  • Full implementation of EcoRestore will occur and alleviate many of the endangered species issues.
  • Water for the environment will not be sacrificed every time there is a water emergency (the co-equal goals promise).

Trusting the operation of the project is a problem because under emergency conditions, such as another severe drought, environmental water could be re-allocated for other uses (e.g., through Temporary Urgency Change Petitions to the State Water Resources Control Board).  An additional worry is the current administration in Washington DC, which shows little concern for environmental issues and endangered species, could apply additional pressure or new regulations to change the water allocation system.

If you don’t trust that WaterFix will be operated as promised, what alternatives do you have? Here some general alternatives:

1. Status quo. This means continuing to rely on ad hoc responses to droughts and floods as well as delaying large-scale infrastructure improvements necessary to accommodate sea level rise, big storm surges, extended drought, and earthquakes. Under this scenario, invasive species will become even more dominant and native species, like smelt, will disappear.  There is room here, of course, for innovative programs that reverse island subsidence, control invasive species, and reverse declining trends in native fishes through large-scale habitat restoration and pulse flow releases from dams.  This will take a visionary effort, led by the Delta Stewardship Council, coordinating the actions of many agencies, a difficult task (See Lund and Moyle 2013 for suggestions on how to do this).

2. Build one tunnel, not two. The idea is to build a single tunnel that has just enough capacity to supply urban water needs or function as an emergency conveyance system when large levee failures or severe drought draws seawater into the Delta.  This could protect California’s urban water supply from catastrophic failure, but from a smelt’s perspective, this is just a step above the status quo, because ultimately the pumps in the South Delta will continue to be relied upon for most water exports (the dual conveyance solution). Cross-Delta movement of water will continue, if somewhat reduced, as will entrainment mortality of native fishes. Presumably, EcoRestore would be at least partially implemented, providing some relief for native fishes.

3. Roll back water delivery volumes to pre-1980 levels. The goal would be increased flows down the Sacramento and San Joaquin Rivers through the Delta and estuary. This would have many positive effects (Cloern et al. 2017) and would be especially beneficial to native fishes, like delta smelt, that require estuarine gradients of temperature, salinity, and water clarity. It would also allow for pulse flows to carry juvenile salmon out to sea and to flood parts of the Yolo Bypass for fish rearing on an annual basis.  Higher flows would also enhance the benefits of restoration projects under EcoRestore.  Unfortunately, given the politics and value of water in California, this option is very unlikely to happen, unless the environment is assigned an inviolable water right to make it truly ‘coequal’ with other water users.

4. Construct a North-South cross-Delta channel with reinforced levees, tidal gates, weirs, and barriers that would deliver Sacramento River water to the South Delta under most situations (see Lund et al. 2010). This version of dual conveyance would anticipate the need for emergency construction of such a facility should levees fail as the result of sea level rise, flooding, land subsidence, and earthquakes, or all four. However, this option would ignore most estuarine ecosystem needs of the Delta, especially if it was operated with little consideration for environmental water during drought conditions.  It could be partially mitigated through EcoRestore, provided the restoration efforts were tied to guaranteed flows down the Sacramento River and through the Delta, at key times.

Each of these four options face common challenges: they have to deal with major changes to the Delta wrought by sea level rise, subsidence of farmed islands in the south and central Delta, increased frequency of large storms/floods, and earthquakes.  While these projections, most featuring levee collapse, may seem alarmist, scientific studies predict large-scale change is going to happen; it’s merely a question of when. Thus, at some point, the south and central Delta will contain large expanses of salty water with reduced tidal influence, ending farming in this region. This new Delta will be a much more difficult place in which to move fresh water to the south Delta pumping plants.  Fish and invertebrates will continue to be abundant but the assemblages are likely to be made up of salt-tolerant forms, such as yellowfin goby, Mississippi silverside, starry flounder, striped bass, northern anchovy, Black Sea jellyfish, and overbite clam.  Lake-like regions might even be seasonally used by Delta smelt, although they will be too warm in summer. Fighting this magnitude of change to keep the status quo will require large investment in levees and barriers, as well as in EcoRestore, making the Delta even more artificial and highly managed than it is today.

So what happens to Delta smelt under these options?  Assuming partial recovery in response to the wet winter of 2016-17, assuming successful supplementation from a smelt conservation hatchery, and assuming EcoRestore and additional measures improve smelt habitat, guided by present Biological Opinions, the extinction of Delta smelt may be prevented.  If the tunnels survive lawsuits and political opposition, their operation is at least 10-20 years in the future. Thus, smelt recovery will have to be well on its way for the tunnels to have a detectable effect.  Meanwhile, the longer we delay, the more likely drastic large-scale emergency measures will be put in place, with little consideration for environmental or recreational needs.

So, the best option for smelt, and other native fishes, especially salmon, is #3, because it should result in a large increase in freshwater flows through smelt habitat (Moyle et al. 2012).  This conclusion is essentially the same as that of the much-ignored Recovery Plan for the Sacramento/San Joaquin Delta Native Fishes (USFWS 1996).  The realities of California water politics, however, dictate that one of the other three options is much more likely to happen. Of these options, the WaterFix + EcoRestore option deals best with future changes to the Delta and seems most likely to keep delta smelt, salmon, and other desirable fishes as part of the Delta ecosystem.  We are past the point where passive management and ad hoc responses to emergencies will keep delta smelt and most other native fishes as participants in the Delta’s ecosystem. Large scale changes require large scale, active management solutions, like WaterFix+EcoRestore.

Peter B. Moyle is a UC Davis Professor Emeritus of fish biology and an associate director of the Center for Watershed Sciences. James Hobbs is a research scientist with the UC Davis Department of Wildlife, Fish and Conservation Biology.

 Further reading

Cloern, J. E., J. Kay, W. Kimmerer, J. Mount, P. B. Moyle, and A. Mueller-Solger. 2017. Water wasted to the sea? San Francisco Estuary and Watershed Science 15(2). jmie_sfews_35738. Retrieved from:

Hanak, E., J. Lund, A. Dinar, B. Gray, R. Howitt, J. Mount, P. Moyle, and B. Thompson. 2011.   Managing California’s Water: from Conflict to Reconciliation.  PPIC, San Francisco. 482 pp.

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.

Lund, J., E. Hanak, W. Fleenor, W., R. Howitt, J. Mount, and P. Moyle. 2007. Envisioning Futures for the Sacramento-San Joaquin Delta. San Francisco: Public Policy Institute of California. 284 pp

Lund, J. R. and P.B. Moyle. 2013. Adaptive management and science for the Delta ecosystem. San Francisco Estuary and Watershed Science 11(3).

Moyle, P.B. 2008. The future of fish in response to large-scale change in the San Francisco Estuary, California. Pages 357-374 In K.D. McLaughlin, editor.  Mitigating Impacts of Natural Hazards on Fishery Ecosystems.  American Fisheries Society, Symposium 64, Bethesda, Maryland.

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 pp.

Moyle, P. B., L. R. Brown, J.R. Durand, and J.A. Hobbs. 2016. Delta Smelt: life history and decline of a once-abundant species in the San Francisco Estuary. San Francisco Estuary and Watershed Science 14(2)

US Fish and Wildlife Service. 1996.  Recovery Plan for the Sacramento-San Joaquin Delta Native Fishes. US Fish and Wildlife Service, Portland, Oregon.  193 pp

This entry was posted in California Water, Conservation, Delta, Fish, Planning and Management, Restoration, Sacramento-San Joaquin Delta, Sustainability and tagged , . Bookmark the permalink.

16 Responses to California WaterFix and Delta Smelt

  1. Stan Wallis says:

    I’ve retired in the water industry from a career (40 years) in the water industry and I understand that it is the non-indigenous bass that are the smelt’s downfall and it is NOT the pumping that is causing the population reduction.


    • Bill Eisen says:

      I can’t imagine how draining additional water from the Sacramento Delta could have a positive effect on the environment especially when much of the water is destined for thirsty central valley almond and pistachio groves which export nuts for consumption in Mexico. The so-called water fix is a boondoggle expected to cost billions. Why not instead spend the money to acquire central valley water rights and encourage central valley growers to take their farms elsewhere where water is more plentiful?


  2. Death Trap “Clifton Court Forebay” with the pumping is the problem. Studies have been done, but replacing 1.5 miles of levee with a 1.5 mile fish screen has not been studied. Keeping all fish out of CCF and in the Delta would eliminate the Death Trap and save money by being able to eliminate the fish capture and relocation facilities.


  3. mcubedecon says:

    An interesting discussion and comparison of the options. But what if WaterFix turns out to be too expensive and not enough water contractors subscribe to make it financially viable?


  4. Delta smelt are not the only likely victims to be claimed by California WaterFix—Delta environmental justice communities have significant numbers of individuals and families with incomes below the 2014 poverty line residing in Antioch, Pittsburg, Clarksburg, Stockton, Sacramento, and West Sacramento.

    In Stockton, residents will have to pay for more intense treatment of degraded drinking water quality due to Tunnels operations in the north Delta, and Delta subsistence fishing would become more hazardous during the 14 years when WaterFix construction occurs due to mercury contamination in Delta sediments.

    Peter Moyle and James Hobbs suggest that if the Tunnels are NOT built, then the best alternative is to “roll back water delivery volumes to pre-1980 levels.” That would mean capping total exports from the Delta at about 3 million acre-feet a year (as opposed to, say, the 6.7 million that were exported in 2011, or the proposed average future export levels of 4.7 to 5.3 put forward in MWD’s white papers – and remember, averages can be skewed by some very high as well as low export numbers).

    But they then say that this is not politically realistic, and that the other three alternatives (status quo, build one tunnel not two, and create a system of reinforced levees, tidal gates, weirs, and barriers etc “that would deliver Sac River water to the south Delta pumps under most situations”) are more realistic.

    On that last point, Delta recreational boaters just announced opposition to the Tunnels and are always all over proposals to block Delta channels for the sake of water supply movement:

    See also RTD’s piece on the failed history of salt water barriers in the Delta at:

    And as to the single tunnel idea, DWR and the water contractors years ago rejected one tunnel (the “portfolio option”) as unworkable for operational/maintenance reasons. That leaves the status quo and rolling back exports, really.


  5. Pingback: California Water News for August 15, 2017

  6. Andres Cano says:

    I am surprised by the elementary error in option 2. “Build one tunnel, not two … for urban needs” This scholar should be well aware that 80% of water from the current system and the tunnels is for farms. This adds to the misconception that the southern cities take all the water.


    • jaylund says:

      One-tunnel options seem potentially quite viable. But smaller tunnel capacity would likely be used mostly for urban areas, due to the better water quality from tunnel than in-Delta diversions.


  7. Missed big issue — Fish Death Trap @ Clifton Court Forebay — replacing the 1 1/2 mile levee at West Channel with 1.5 mile fish screen would slow export water to no longer kill fish while exporting water. Flows can be restored if pumping is 24/7 but filling CCF is done only at night and flows are returned to normal during day time.


  8. As a layman on this subject, so I beg your forgiveness. That said, I am concerned with the new’s, ‘gloome and doome’ nead’s glue, not to old to learn.


  9. Tim McCabe says:

    Desalination is the answer. We need to build desalination plants in L.A. but they don’t want them there ugly, so lets continue to rape the delta. Lets put contaminated muck piles and claim we are fixing the levies. I live here in the delta and 16 years they increased the pumps at the Clifton for-bay 5 times more powerful and now the San Joaquin river floes backward. The delta is in pearl and the cause is directly because of over pumping to send water to L.A.
    The metropolitan water raped the Owens Valley and turned it in to Dust Bowl , and now they want to turn the Sacramento river into Sacramento Creek. This will be the death of the delta.
    Tim McCabe


  10. SF Al says:

    LA managed to mess up Owens Valley with their water greed. Now they are after our Northern California Delta water. This seems to be a no brainer. The LA water grab has damaged
    us enough already. Recycle more in LA. Use mother nature to DeSal water. Come On LA, prove you are a member of California. TEAM up avoid destroying San Francisco Delta water supply by your greed.


  11. Richard Hempfer says:

    Southern CA should be building desalinization plants instead of sucking more water out of the delta. Regarding the canal that ships delta water to LA: I would also like to see a study done to determine how much water is lost to evaporation from the parts of the canal that is open to the sky. .


  12. Chris Gilbert says:

    The Uncertainties section is enough to convince me that it shouldn’t be done. Too much at risk.
    And while rolling back exports may seem politically infeasible, recognizing that 80% of diverted water is for agriculture and that much agricultural land in the western part of the Valley is in poor soils, and that the U.S. has already negotiated land there to be fallowed in exchange for debt forgiveness to Westlands, and furthermore, that much of the produce is exported out of the country benefiting in large part a handful of hedge funds, big corporations and other large investors but providing jobs among the lowest paying in the state, there is plenty of room for retirement of agricultural land, esp. given that that industry only contributes about 2% to the state’s GDP and the same % to it’s job pool. It’s time to think of Calif. as less an agricultural behemoth and more urban, high tech, etc.


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