Estuaries provide critical habitat for a vast array of fish and wildlife but are also a nexus for core economic activities that mobilize and concentrate contaminants that can threaten aquatic species. Selenium (Se), an essential element and potent reproductive toxin, is enriched in parts of the San Francisco Estuary (SFE) to levels known to cause toxicity, yet the risk of Se to species that inhabit the SFE is not well understood. We quantified Se concentrations in muscle, liver, and ovary of the demersal cyprinid Sacramento Splittail from six regions in the SFE at three time points (fall 2010-11, spring 2017) to evaluate Se exposure risk. Here we report fish morphological attributes, total selenium concentrations in fish boneless skinless muscle, liver, and ovary, as well as carbon, nitrogen and sulfur stable isotope values and elemental mass concentrations in fish muscle.