Unlike conventional flood control systems that frequently isolate rivers from ecologically-essential floodplain habitat, California's Yolo Bypass has been engineered to allow Sacramento Valley floodwaters to inundate a broad floodplain. From a flood control standpoint, the 24,000 ha leveed floodplain has been exceptionally successful based on its ability to convey up to 80% of the flow of the Sacramento River basin during high water events. Agricultural lands and seasonal and permanent wetlands within the bypass provide key habitat for waterfowl migrating through the Pacific Flyway. Our field studies demonstrate that the bypass seasonally supports 42 fish species, 15 of which are native. The floodplain appears to be particularly valuable spawning and rearing habitat for the splittail (Pogonichthys macrolepidotus), a federally-listed cyprinid, and for young chinook salmon (Oncorhynchus tshawytscha), which use the Yolo Bypass as a nursery area. The system may also be an important source to the downstream food web of the San Francisco Estuary as a result of enhanced production of phytoplankton and detrital material. These results suggest that alternative flood control systems can be designed without eliminating floodplain function and processes, key goals of the 1996 Draft AFS Floodplain Management Position Statement.