The dataset accompanies Figures 2–4 of Matchett and Fleskes (2018) and therein the subject data are referenced as "Table A1". Data summarize peak abundance (km2) of Central Valley waterbird habitats (i.e., wetland and flooded cropland types) that are available between August and April (of the following year) for each of 17 projected scenarios by planning basin, scenario, and habitat. Area of each habitat for each scenario-basin combination is provided for the month when the most area of the respective habitat is typically flooded and available for waterbird use (i.e., January for all wetlands and winter-flooded rice and corn, and September for other winter-flooded crops in Tulare Basin). The dataset also includes relatively recent (year 2005) area of habitat (i.e., “existing_km2”) for comparison with habitat areas based on scenarios. Flooded cropland habitats are defined as winter-flooded rice, winter-flooded 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). This dataset includes results for eight of nine basins defined by the Central Valley Joint Venture in the Central Valley Joint Venture Implementation Plan (2006); subject basins are the Colusa, Butte, Sutter, American, Yolo, Delta, San Joaquin, and Tulare Basins (Suisun Basin excluded). Data on availability of waterbird habitats is summarized by planning basin, scenario, habitat, and month in 5 metrics (in addition to recent historical area): the least available area; areas available in ≥ 25%, ≥ 50%, and ≥ 75% of years; and maximum available area. 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