The dataset summarizes total area (km2) and proportion of Central Valley waterbird habitat, summed across individual waterbird habitats (i.e., wetland and cropland types), that was available for each of 17 projected scenarios. The dataset also includes relatively recent (year 2005) area of existing habitat (i.e., “existing area”) for comparison with areas based on scenarios. Analysis was conducted for the projection period including water-years 2006–2099 (water-year defined as October-December and January–September of the following year). Because habitat areas vary through the season with timing of crop harvest and flooding of wetlands and post-harvested fields, annual areas and proportions represent summation of available projected habitat area following completion of crop harvest and flooding of wetland and crop habitats during the season. Cropland habitats are defined as winter-flooded rice, unplowed dry rice, winter-flooded corn, unplowed dry corn, and other winter-flooded cropland (in Tulare basin). Wetlands are defined as summer-irrigated seasonal wetland, seasonal wetland that is not summer-irrigated, and semipermanent wetland (combines semipermanent and permanent wetland types). These data are used to support the following publication: Matchett EL, Fleskes JP (2017) Projected Impacts of Climate, Urbanization, Water Management, and Wetland Restoration on Waterbird Habitat in California’s Central Valley. PLoS ONE 12(1): e0169780. doi:10.1371/journal.pone.0169780