The Central Valley of California provides important breeding habitat to numerous species of wetland-dependent birds, despite the loss of over 90% of naturally occurring wetlands. A majority of shorebirds breeding in this region rely on shallow-flooded habitat adjacent to sparsely vegetated uplands as provided by rice (Oryza sativa), managed wetlands, and other habitats. We estimated the current extent of potential breeding shorebird habitat provided by rice and managed permanent and semi-permanent wetlands in each of four major planning regions of the Central Valley, and estimated the average breeding densities and current population sizes of two species of shorebirds: the Black-Necked Stilt (Himantopus mexicanus) and American Avocet (Recurvirostra americana). Using a population status framework based on principles of conservation biology, we estimated that stilt populations are small (<10,000 individuals) or very small (<1,000 individuals) in three of the four planning regions, and avocet populations are small or very small in all four planning regions. We then used the framework to define long-term (100-year) population objectives for stilts, avocets, and a third species, Killdeer (Charadrius vociferous), designed to meet our long-term conservation goal of supporting self-sustaining, genetically robust, and resilient populations of breeding shorebirds in the Central Valley. We also estimated the long-term species’ density and wetland habitat objectives necessary to achieve the population objectives for all three species. The corresponding short-term (10-year) conservation objectives are to restore semi-permanent wetlands to provide an additional 11,537 ha (28,508 ac) of habitat for breeding shorebirds (by planning region: 2,842 ha in Sacramento, 2,897 ha in Yolo–Delta, 2,943 ha in San Joaquin, and 2,855 ha in Tulare), and to enhance existing habitat to support density objectives. Our approach provides a transparent, repeatable process for defining science-based conservation objectives for breeding shorebirds and their habitats in the Central Valley, which can help unite stakeholders around common goals and motivate conservation actions.