The reduced delivery of Colorado River water to the Imperial Valley, California, has resulted in the shrinking of the Salton Sea. The Salton Sea is primarily sustained by irrigated agricultural runoff which has created wetland habitat along the newly exposed lakeshore. Wetlands receiving irrigation runoff are at risk of selenium bioaccumulation which may cause reduced survival and developmental abnormalities of wetland-obligate birds like the federally endangered Yuma Ridgway’s rail (Rallus obsoletus yumanensis). We captured breeding rails from 2020–2025 and compared rail selenium levels within three marsh types (fed with irrigation runoff, Colorado River water, or spring water). We collected blood, breast feathers, and head feathers of rails in all three water sources for selenium comparisons. We tagged adult rails with GPS transmitters to locate nests and foraging locations where we collected eggshells, unhatched eggs, and prey species. Selenium concentrations varied among the three marsh types. Selenium concentrations were highest in agricultural-fed marshes compared to river-fed and spring-fed marshes. Our results suggest that increased input of Colorado River water into agricultural-fed marshes that support Yuma Ridgway’s rails may reduce the dietary risk of selenium bioaccumulation to rails.