Reconciling fish and fowl with floods and farming

Rice fields on the Yolo Bypass. Photo by Carson Jeffres, UC Davis

Rice fields on the Yolo Bypass, an engineered floodplain of the lower Sacramento River. Photo by Carson Jeffres, UC Davis

By Robyn Suddeth

Floodplains are extremely productive habitats for native fish and birds, yet floodplains in California are cut off from rivers by levees and development. The loss of this severed habitat threatens many native species that evolved to take advantage of seasonal flooding.

Ecologists’ traditional approach to this problem would be to recreate some of the historical floodplain by restoring natural flows and vegetation. In much of California, however, levees, dams and riverside development make restoration impractical.

Recognizing these constraints, reconciliation ecology encourages land and water managers to re-engineer human-dominated landscapes to be more hospitable for native species without significantly diminishing human uses.

California’s Yolo Bypass, an engineered floodplain on the Sacramento River, is an excellent case study of this new approach to native species conservation.

As a doctoral student with the UC Davis Center for Watershed Sciences I recently developed a computer model to balance economic and ecological goals in the bypass under a range of habitat quality assumptions.


The Yolo Bypass conveys floodwaters from the Sacramento, American and Feather river systems. Blue circles mark the western tributaries. Green arrows shows inflows from the Sacramento River. Source: Suddeth, R., 2014. p. 92

Results from this Yolo Bypass Multi-Objective Optimization Model suggest that significant habitat improvement is possible for several fish and bird species at little or no cost to farmers. Further, farming can actually create and in some cases even enhance habitat for fish and birds.

The U.S. Army Corps of Engineers built the bypass more than 80 years ago to protect Sacramento and the southern Sacramento Valley from floods. It lies within the Sacramento River’s historical floodplain and is connected to the river by several weirs. Three miles wide and 40 miles long, the 59,000-acre floodway can carry up to four times the flow of the river’s main channel during large floods.

But the bypass serves several additional economic and ecological purposes: farming, duck hunting, wetland for water birds and shorebirds, and spawning and rearing grounds for several fishes — including endangered spring- and winter-run Chinook salmon.

In the past decade, resource managers and scientists have shown increasing interest in the bypass’ functionality as fish habitat during floods. Studies have shown that young Chinook salmon grow much faster in flooded rice fields on the bypass than they do in the main river channel. The bypass has been widely hailed as the most promising site in the Central Valley for restoring floodplain habitat for fish. The Bay Delta Conservation Plan proposes a notch in the upstream Fremont Weir to increase the frequency and duration of inundation at key times for salmon and Sacramento splittail.

 by Carson Jeffres

In an ongoing salmon-rearing experiment, researchers have found juvenile Chinook planted in flooded rice fields after harvest grow phenomenally faster and fatter than those left to mature in the Sacramento River  — bolstering the hypothesis that access to a floodplain is important to sustaining salmon populations.  Photo by Carson Jeffres

These increased flows are not without controversy. While farming and wetland management on the bypass is adapted to occasional winter flooding, water that stays on fields too long into the spring can delay drawdown for wetland plants that birds feed on, or delay planting of crops. Either way, the growing season is shortened and crop yields reduced, cutting into waterfowl food and farm income.

Flooding the bypass for the benefit of farms, fowl and fish will require a carefully scheduled and controlled low-flow inundation of fields and some landscape re-engineering. Many decisions would need to be made at varying times and places, all with different consequences for each management objective.

Multi-objective optimization models like the one developed for this study can integrate large amounts of data and knowledge and account for the relationships and tradeoffs among different objectives. This is especially useful in reconciliation planning where many uses and variables interact on a landscape and for re-engineering, where many decisions must be considered simultaneously.  

The study used the Yolo Bypass Multi-Objective Optimization Model to test land and water management decisions and maximize net revenues for varying levels of fish and bird habitat quality.


Results of a computer optimization model analysis show that fish and bird habitat on the Yolo Bypass can be improved with little annual costs for farmers. The graph plots habitat quality tradeoffs for fixed annual economic losses, with a Feb. 7 start for flooding and varied habitat assumptions and priorities (salmon and dabbling ducks prioritized on left and all land uses weighted equally for fish on right). Blue area shows where tradeoffs among fish, birds and annual revenues are low for significant gains in habitat quality. Source: Suddeth, R., 2014, p. 111

As for land use, model results suggest that habitat quality could be improved most efficiently by shifting from pasture to seasonal wetland, mostly in the southern bypass. This result persisted under a broad set of runs with varying habitat quality assumptions. Results also often indicated that small additions in rice acreage could improve fish and bird habitat.

Habitat quality and economic performance on the bypass are not solely functions of land use ; they also depend on the extent, timing, duration and depth of flooding. Gates, inflatable dams and other flow-directing structures can manipulate these variables to maximize habitat quality at least cost to farmers.

Following the guidelines listed below, increased flows from a notched weir could create fish habitat and improve bird habitat quality relative to current dry years with no annual revenue losses for farmers or duck club owners. Significant improvements in habitat quality are achievable with additional land-use changes and $100,000 – $200,000 in annual net revenue losses. These losses amount to less than 1 percent of total annual crop revenues on an economically optimized (modeled) bypass, and a loss of 1 – 5 percent of the actual annual farm revenues in 2005 – 2009.

Trading pasture for wetlands or adding acres of rice will have tax implications for Yolo County and financial implications for local farmers and landowners. None of these management changes can occur without first designating who pays for these environmental benefits. The optimization model can help provide detailed and zone-specific information about the economic implications of management decisions and a rough estimate of ecological gains or losses from any changes.

Another potentially required land-use change would be the creation of new wetlands and fields devoted to habitat-friendly crops. Locating these lands close together and near the water source will allow applied water to be more easily managed for depth and duration.

There is much promise for a reconciliation approach to management of the Yolo Bypass that is not costly to farmers and landowners. Crops are a vital component of the overall habitat mosaic – a sign that even heavily modified floodplains like the bypass can be improved for native species without substantially diminishing human use.

Robyn Suddeth currently works as a water policy analyst at CH2M Hill. She can be reached at


Guidelines for managing flood flows for six to eight weeks on Yolo Bypass  

  • Timing.  Under almost all habitat quality assumptions, the best start date for a six- to eight-week inundation lies somewhere in the last week of January or the first few weeks of February. This timing gives farmers a long growing season and best balances the needs of all four species groups. The best start date also depends on duration of flooding. For example, flooding in early February would not significantly benefit shorebirds unless it lasts at least six weeks. The shorter the duration, the more important timing becomes for each species and the harder it is to strike a balance with just one flood event. 
  • Depth.  Inundation depth, which varies in space and time during the flood, is the one management decision for which general conclusions are difficult. Depth controls exactly when and where a particular species will have viable habitat within the larger flood mosaic, so small changes in preferences can make a large difference in the optimal pattern. In general, a bypass balanced for fish and birds will benefit most from an inundation that starts sometime in late January or early February with (1) shallow flooding during the first few weeks, usually less than 8 inches for birds; then (2) deeper flooding for the next few weeks (13 – 18 inches) to provide better fish habitat; followed by (3) a mixture of mudflat to moderately deep habitats as waters recede and shorebirds begin to share the system with fish and dabbling ducks. This is the case even for February flooding that spans only six weeks. 
  • Duration.  If flooding begins before the last week of February, then it is always valuable – and not necessarily costly – to keep at least some water on wetlands and other lower-value land uses for a full eight weeks if possible. When the computer-simulated flooding was shortened by two weeks, attainable habitat quality decreased by about 25 percent. Long floods increase the availability of flooded habitat to satisfy a wider variety of species preferences.
  • Hydraulic management.  The ability to control the flood footprint throughout the inundation event can significantly increase the cost-effectiveness of flooded habitat quality improvements. Hydraulic management could direct most flooding to the southern bypass where agricultural losses are less. Rice and safflower fields should be drained by mid-March for planting. Flooded rice fields are especially good at producing invertebrates, a staple for fish and birds. Most of the production occurs early during inundation and is fairly self-sustaining. Drainage from these fields could be directed to wetlands and pasture so fish and birds can continue to feast on the bounty.

    Delaying crop planting beyond mid-March could significantly reduce crop yields and revenues in the Yolo Bypass. Source: Suddeth, 2014, Executive Summary

    Delaying crop planting beyond mid-March could significantly reduce crop yields and revenues in the Yolo Bypass. Source: Suddeth, 2014, Executive Summary


Further reading

Fleenor, W. Suddeth, R. Oct. 18, 2013. Innovations in floodplain modeling: A test drive on the Yolo Bypass. California WaterBlog

Howitt, R., MacEwan, D., Garnache, C., Medellin-Azuara, J., Marchand, P., Brown, D., Six, J., Lee, J. 2013. Agricultural and Economic Impacts of Yolo Bypass Fish Habitat Proposals. Prepared for Yolo County. 58p

Howitt, R., J. Medellin Azuara. May 19, 2013. A sweet spot for farms and fish on a floodplain, The Davis Enterprise

Jeffres, C. June 2, 2011. Frolicking fat floodplain fish feeding furiously. California WaterBlog

Mount, J. Aug. 11, 2011. The Benefits of Floodplain Reconnection. California WaterBlog

Sommer, T., B. Harrell, M. Nobriga, R. Brown, P. Moyle, W. Kimmerer and L. Schemel. 2001. “California’s Yolo Bypass: Evidence that flood control can be compatible with fisheries, wetlands, wildlife and agriculture,” Fisheries 26 (8)

Suddeth, R. 2014. Multi-Objective Analysis for Ecosystem Reconciliation on an Engineered Floodplain: The Yoloi Bypass in California’s Central Valley. PhD dissertation. UC Davis

Suddeth, R. 2014. Reconciling fish, birds and farming on California’s Yolo Bypass. Executive summary prepared for the Delta Stewardship Council.

U.S. Department of Interior, et al. 2013. Bay Delta Conservation Plan, Draft EIR/EIS. Chapter 3, Part 1: Conservation Strategy

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9 Responses to Reconciling fish and fowl with floods and farming

  1. Greg Giusti says:

    Well written and thoughtful piece. I’m often surprised how similar articles often focus and justify the economic loss of farm land but seldom discuss the upside of an improved commercial and recreational fishery. In our economy and culture where a great deal of disposable income is directed toward environmental recreational activities the potential increase in both waterfowl and salmonids revenues from increased opportunities should be considered in economic assessments.
    At the very least I hope folks look at your efforts seriously.


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