Matchett and Fleskes (2018) evaluated availability of wetland and agricultural habitats used by waterbirds overwintering in the Central Valley of California under 17 scenarios of projected climate, urbanization, and water supply management (for more information about scenarios see scenario description and Table 1 in Matchett and Fleskes [2018]). Central Valley waterbird habitats investigated in this research included managed flooded wetlands and croplands and dry cropland habitats. Flooded cropland habitats are defined as winter-flooded rice, winter-flooded corn, and other winter-flooded cropland (in Tulare basin). Flooded wetlands are defined as summer-irrigated seasonal wetland, seasonal wetland that is not summer irrigated, and semi-permanent wetland (combines semipermanent and permanent wetland types). Dry cropland habitats include unplowed dry corn and unplowed dry rice fields. Two datasets documented herein accompany Matchett and Fleskes (2018), and for each of the 17 scenarios, these datasets summarize available area (km2) of each habitat during August–April (of the following year). The first of these datasets, “Table A1” (also referenced as Table A1 in Matchett and Fleskes [2018]), corresponds with areas of available habitat in Figures 2–4 of Matchett and Fleskes (2018). Table A1 summarizes available area (km2) of each flooded habitat by planning basin and scenario when available habitat area is typically highest during the wintering period. The second dataset, “Table A2” (also Table A2 in Matchett and Fleskes [2018]), corresponds with areas of available habitat in Figure S1 of Matchett and Fleskes (2018), and summarizes areas of each flooded and dry waterbird habitat by planning basin, scenario, and month during the wintering period. These data support the following publication: Matchett EL, Fleskes JP. 2018. Waterbird habitat in California’s Central Valley basins under climate, urbanization, and water management scenarios. Journal of Fish and Wildlife Management. Online early. doi:10.3996/122016-JFWM-095