Critical habitat for millions of migratory birds that rely on them as breeding, wintering and stopover sites along the Pacific Flyway, California has lost over 90% of its wetlands in the past two centuries. Among the most important remaining sites is the Salton Sea, California’s largest lake and hosts to some of the largest waterbird concentrations in the Western United States. However, the Sea is shrinking rapidly due to reduced inflows, triggering significant changes in habitat and food availability. We analyzed seven years (2016–2023) of bird surveys, habitat, and water quality assessments to evaluate how birds are responding to the Sea’s rapidly changing environment. Key findings show that while deep-water habitats and fish-eating birds like pelicans and cormorants are in decline, shallow wetland habitats are expanding by 23% from 2019 to 2022, supporting significant gains in shorebird populations, including Least and Western Sandpipers. Overall, waterbird numbers increased by roughly 15% annually during the study period, underscoring the Sea’s continued ecological value. Our research identifies new opportunities for conservation and restoration with new emerging and expanding habitats. With coordinated action, the Salton Sea can remain a resilient refuge for birds and a healthier environment for surrounding communities.