Across the Central Valley of California, millions of wintering waterfowl rely on moist soil seed (MSS) plants that grow in managed seasonal wetlands as a critical source of food. Estimates of MSS plant production are used to set waterfowl habitat targets yet this information is not well known. We created the first Central Valley-wide time series maps of MSS plant distributions and productivity. We found that MSS plant seed yield declined in critical drought years, which corresponded with reduced water delivery to managed wetlands. Our results provide improved food resource estimates and information to help managers prioritize actions as water supply becomes more uncertain with climate change.