Biodiversity loss from agricultural intensification underscores the urgent need for science-based conservation strategies to enhance the value of agro-ecosystems for birds and other wildlife. California’s Central Valley, which has lost over 90% of its historical wetlands and currently is dominated by agriculture, still supports waterbird populations of continental importance. A better understanding of how waterbirds use available habitat is particularly needed in the Sacramento–San Joaquin Delta, an ecosystem under threat. From 2013 to 2015, we studied waterbird habitat associations in the Delta during fall migration and winter by conducting diurnal counts at random locations in key waterbird habitats throughout the Delta. Waterbird use of cover types (agricultural crops and managed wetlands) varied substantially among waterbird groups, by season, and among geographic sub-regions of the Delta. Overall, wetlands were particularly important to waterbirds in fall. In winter, wetlands and flooded rice and corn were important to many waterbird groups, and non-flooded corn and irrigated pasture to geese and cranes. The factors that influenced waterbird abundance and distribution also varied substantially among groups and differed at various geographic scales. In both seasons, most groups had a positive association at the field level with flooded ground and open water, and a negative association with vegetation. Given the great uncertainty in the future extent and pace of habitat loss and degradation in the Delta, prioritizing the conservation actions needed to maintain robust waterbird populations in this region is urgent. For the Delta to retain its importance to waterbirds, a mosaic of wetlands and wildlife-friendly crops that accounts for the value of the surrounding landscape must be maintained. This includes restoring additional wetlands and maintaining corn, rice, alfalfa, and irrigated pasture, and ensuring that a substantial portion of corn and rice is flooded in winter.