Selenium bioaccumulation in wetlands fed from agricultural drains can negatively affect reproductive success in waterbirds. The Salton Sea, California, is primarily fed by agricultural drainage water that has created emergent wetlands along the lakeshore, home to the federally endangered Yuma Ridgway’s rail (Rallus obsoletus yumanensis). We captured rails during the 2020–2023 breeding seasons and compared nesting success and egg hatching rates among different water sources: irrigation runoff, Colorado River water, or groundwater. We tagged adult rails with satellite GPS transmitters and used GPS data to locate nests and monitor nest attendance patterns. We compared selenium levels in eggshells and eggs that failed to hatch (egg content). We compared the egg fail-to-hatch rate, the egg infertility rate, and the rate of fetal abnormalities among the 3 water sources. Ag-fed marshes had a lower nesting success rate and higher average selenium concentrations in unhatched eggs. River-fed marshes had a higher egg fail-to-hatch rate and infertility rate. No fetal abnormalities were detected in unhatched eggs, but embryo malpositioning was noted in 2 eggs. Our results suggest that supplying marshes with Colorado River water rather than agricultural drainage water could reduce the risk of selenium bioaccumulation and increase the nesting success of rails.