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Differences in basal carbon sources, invertebrate density and salmon growth rate were observed in food webs across a lateral transect of aquatic habitats in the Sacramento River Valley, California. Similar to many large river valleys globally, the Sacramento River Valley has been extensively drained and leveed, hydrologically divorcing most floodplain wetlands and off-channel aquatic habitats from river channels. Today, the former floodplain is extensively managed for agriculture and wildlife habitat. Food web structure and juvenile Chinook Salmon (Oncorhynchus tshawytscha) growth were compared in three aquatic habitat types–river channel, a perennial drainage canal in the floodplain, and agricultural floodplain wetlands, which was seasonally inundated to provide bird and fish habitat during the non-agricultural growth season (late winter). Zooplankton densities on the floodplain wetland were 53 times more abundant, on average, than in the river. Juvenile Chinook Salmon raised on the floodplain wetland grew at mm/day, a rate 5x faster than fish raised in the adjacent river habitat (0.18 mm/day). Mean water residence times calculated for the floodplain agricultural wetland, perennial drainage canal and Sacramento River were 2.15 days, 23.5 seconds, and 1.7 seconds, respectively. Carbon in the floodplain wetland food web was sourced primarily through heterotrophic detrital pathways while carbon in the river was primarily autotrophic and sourced from in situ phytoplankton production. Hydrologic conditions typifying the ephemeral floodplain-shallower depths, warmer water, longer residence times and detrital carbon sources compared to deeper, colder, swifter water and an algal-based carbon source in the adjacent river channel-appear to facilitate the dramatically higher rates of food web production observed in floodplain verses river channel habitats. These results suggest that hydrologic patterns associated with winter flooding provide Mediterranean river systems access to detrital carbon sources that appear to be important energy sources for the production of fisheries and other aquatic resources.