Experimental Habitats for Hatchery Delta Smelt

by Peter Moyle

Borrow pit on Bouldin Island that is now a pond maintained by ground water inflow. If expanded and deepened, and carefully managed, such ponds could become temporary rearing habitat for delta smelt. Photo by Peter Moyle.

The Delta smelt is either extinct in the wild or close to it; in the past year only a handful have been caught, with great effort. In contrast, the UC Davis Fish Conservation and Culture Laboratory (FCCL) has considerable success spawning and rearing the smelt in captivity. This coming winter, the FCCL will have as many as 40,000 smelt ready for release, when temperatures are low and the smelt are likely to spawn naturally. Such releases will be ‘experimental’ so not subject to the take provisions of the federal Endangered Species Act. In this blog, I support the concept that success of re-establishing smelt in the wild requires using multiple approaches.  In previous blogs and papers (Börk et al. 2020, Stompe et al. 2021), the idea of planting hatchery smelt in selected reservoirs was discussed. Here I first explore the problems of releasing fish back into the Delta and then describe an experimental reintroduction project taking advantage of the characteristics of Delta islands.

What do you do with 40,000 smelt?

It is a big question as to what to do, exactly, with 40,000 hatchery smelt. This is the job of the interagency Culture and Supplementation of Smelt Steering Committee (CASS) that has also has to deal with obtaining the many permits needed for any kind of release (CEQA, ESA etc.). Permitting will be a barrier to any action unless CASS decision makers are able to make risky decisions in short periods and get rapid action on the permits. My impression is that CASS prefers to use most of the fish for experimental releases, either as a one-time introduction of all fish or as series of smaller introductions made at selected sites where conditions appear favorable.  There are a number of problems with this approach:

  • The current Delta environment seems unsuitable for wild smelt. Cultured smelt will face the same problems as wild smelt, resulting in low survival. Börk et al. (2020) show that the factors put forth in the USFWS Biological Opinion as supporting recovery of smelt populations don’t hold up under close scrutiny.
  • Keeping track of even 40,000 small smelt in the big Delta is extremely difficult, if not impossible, given the small size of the smelt.
  • Hatchery smelt are genetically and behaviorally adapted for life in an aquaculture facility, so it is doubtful they will be able to quickly adjust to being released into a more natural environment. 
  • A strategy focusing on experimental releases into the Delta does not diversify risks but instead seems to be “putting all the eggs in one basket”.

Alternative: island ponds

Figure 1. Conceptual model of island experimental Delta smelt pond (diagram by Kelly Schmutte).

Mount and Twiss (2005) published a provocative analysis that showed most Delta islands (polders) were below sea level and were continuing to subside. Given weak levees, these polders are subject to sudden flooding, with huge costs to reclaim the land. But viewing flooded islands as habitat for fishes, including delta smelt, struck a number of biologists, including me, as a vision worth exploring. One variant of this idea was to deliberately flood islands and have gated openings so the water could be managed. This variant was not original, in that a private company called Delta Wetlands had actually purchased islands to flood them for water storage. While these big schemes never came to fruition, the idea of using flooded islands for fish conservation continued to be of interest. The version presented here proposes smaller, more manageable habitats, essentially large ponds, on subsided islands. This version developed through several Zoom meetings and involved scientists from Metropolitan Water District, UC Davis, and US Geological Survey.

The basis for this project is the need to spread risks for smelt introductions and to build a controlled food-rich habitat for conditioning hatchery smelt for improved survival in the wild. If this project is successful, it may be possible to propagate smelt in more or less natural ponds until the Delta ecosystem, or parts of it, has improved enough to support smelt on their own. The project is based on research, including findings of Jon Burau and others at USGS, on the hydrodynamic interactions between marsh and pelagic environments. The project includes ponds which are hydrologically-connected to artificial tidal marshes of varying sizes within a 43-acre plot on the northwest corner of MWD’s Bouldin Island (Figure 1, above).

Under current plans, one marsh-pond complex will be operated with water levels that will be raised and lowered for maximum night-time cooling; preliminary modelling by MWD indicates that under present conditions, water temperatures during the hot days of summer can be kept at or below 20°C. A second marsh complex will be operated to maintain maximum residence time for food (zooplankton) productivity. The ponds will be supplemented with cold, aerated groundwater (usually <17° C) during hot months in order to maintain water temperatures sufficient for a Delta smelt growth and survival. Temperature modelers at MWD are confident that sufficient design features can be developed to maintain appropriate conditions for smelt. Furthermore, bioenergetic studies of fish show that a robust food supply, which the project will include, can help compensate for the elevated metabolism of fish living in warmer water than might seem optimal. Finally, this site allows for the research and monitoring necessary for successful smelt supplementation efforts and Delta-wide tidal marsh design parameters. For example, the project could be useful for evaluating acclimation and release methods (particularly of early life stages, hatching frames, and mesocosms) and practices to reduce domestication selection through rearing in a more natural environment.

Figure 2. Drone photo of Bouldin Island, showing site of potential ponds for rearing Delta smelt. The existing facilities in the lower right foreground are eight experimental pools for examining (among other things) how floating mats of tules could provide a supply of invertebrates as smelt food.  New pools could be constructed immediately adjacent to these floating marshes as a near-term, cold weather conditioning facility while a permanent marsh-pond complex is being constructed in the center of the photo. The field in the center could be used in various ways to create ponds for Delta smelt rearing. The lighter colored area upslope of the pond site and edged by the dark green growths of blackberries, could be converted into marshes that drain into the ponds, as in Figure 1. The island is subsided so the ponds are about 20 feet below sea level. Sea level is the surface elevation of the water in the surrounding channels. Photo from Russ Ryan, MWD.

While MWD developed and funded the initial ‘proof of concept’ project, smelt stakeholders and experts will need to work together for the planning, funding, permitting, and monitoring of the project if the project is to succeed. It is urgent that a collaborative effort be made so that a project using 2000 or so hatchery smelt can be possible by the end of this year.   Assuming smelt are available, the project would be on-going in 2022. Time is of the essence, given uncertainties about the status of the smelt.  However, it is worth noting that the facilities and information produced as part of this project can also be applied to saving other native fish species in decline: splittail, Sacramento perch, longfin smelt, hitch, and tule perch.


This pond project here has been presented in a positive light. But it is a high risk project for smelt because it involves creating new habitats by moving dirt and water around, on a subsided island. Such islands have a history of being flooded through levee failure, with additional risks caused by sea level rise, major flood events, and earthquakes. Climate change and drought may make water temperatures warmer than expected.  One way or another, it is likely that the created habitats will be invaded by non-native fishes such as Mississippi silverside. But any project in the Delta, including a straight-forward smelt re-introduction project, faces these same or similar problems; they will have to be dealt with in creative ways. The alternate path of doing nothing or doing too little leads to extinction.


There is well-established precedence for the use of ponds in supplementation strategies of listed fish species as well as for Delta Smelt experimentation. The endangered Rio Grande Silvery Minnow is propagated in earthen ponds prior to release in the wild. The endangered Razorback Sucker is also grown out in seminatural and natural ponds before stocking, a practice which has improved growth rates and subsequent survival in the wild. Aquaculture ponds at the U.C. Davis Center for Aquatic Biology and Aquaculture have been employed extensively in research on Delta Smelt physiology and field trials in species-specific enclosures. 


Re-establishing Delta smelt in its native Delta using hatchery smelt is an extremely difficult task, given how completely the habitat has been altered (Stompe et al 2001). Releasing fish directly into the wild is very risky and success will be hard to determine. Alternative projects need to be developed to spread risk. The Polder Pond Project proposed here is one such project. It proposes to rear Delta smelt in large ponds on a Delta island, on natural foods, which should prepare the fish better, at larger sizes, for release into the wild. The project also entails some risk for the Delta smelt needed for the project (ca. 2,000/year) but even if the smelt fail to adapt well to the ponds, useful information will be obtained on restoring native fishes to the Delta.


Bixby, R., and A. Burdett. 2013. Annual report 2011-2012; Resource utilization by the Rio Grande silvery minnow at the Los Lunas Silvery Minnow Refugium. Available at: ose.state.nm.us

Börk, K., Moyle, P., Durand, J., Hung, T., Rypel, A. L. 2020. Small populations in jeopardy: delta smelt case study. Environmental Law Reporter, 50(9), 10714-10722

Caldwell, C.A., Falco, H., Knight, W., Ulibarri, M., and W.R. Gould. 2019. Reproductive potential of captive Rio Grande Silvery Minnow. North American Journal of Aquaculture 81:47-54.

Day, J.L., Jacobs, J.L., and J. Rasmussen. 2017. Considerations for the propagation and conservation of endangered Lake Suckers of the western United State. Journal of Fish and Wildlife Management 8:301-312.

Mount J. and R. Twiss, 2005. Subsidence, sea level rise, seismicity in the Sacramento-San Joaquin Delta. San Francisco Estuary and Watershed Science. Vol. 3, Issue 1 (March 2005), Article 5. http://repositories.cdlib.org/jmie/sfews/vol3/iss1/art5.

Stompe. D., T. O’Rear, J. Durand, and P. Moyle. 2021 Home is where the habitat is. California WaterBlog  https://californiawaterblog.com/2021/07/04/home-is-where-the-habitat-is/

Watson, J.M., Sykes, C., and T.H. Bonner. 2009. Foods of Age-0 Rio Grande Silvery Minnows (Hybognathus amarus) reared in hatchery ponds. The Southwestern Naturalist 54:475-479.

Peter Moyle is Distinguished Professor Emeritus at the Center for Watershed Sciences, University of California, Davis.

About Andrew Rypel

Andrew L. Rypel is a Professor and the Peter B. Moyle and California Trout Chair of coldwater fish ecology at the University of California, Davis. He is a faculty member in the Department of Wildlife, Fish & Conservation Biology and Director of the Center for Watershed Sciences.
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