Elevated selenium (Se) concentrations in surface water and groundwater have become a concern in areas of the Western United States due to the deleterious effects of Se on aquatic ecosystems. Elevated Se concentrations are most prevalent in irrigated alluvial valleys underlain by Se-bearing marine shales where Se can be leached from geologic materials into the shallow groundwater and surface water systems. This study presents groundwater chemistry and solid-phase geochemical data from the Uncompahgre River Basin in Western Colorado, an irrigated alluvial landscape underlain by Se-rich Cretaceous marine shale. We analyzed Se species, major and trace elements, and stable nitrogen and oxygen isotopes of nitrate in groundwater and aquifer sediments to examine processes governing selenium release and transport in the shallow groundwater system. Groundwater Se concentrations ranged from below detection limit (< 0.5 μg L^− 1) to 4070 μg L^− 1, and primarily are controlled by high groundwater nitrate concentrations that maintain oxidizing conditions in the aquifer despite low dissolved oxygen concentrations. High nitrate concentrations in non-irrigated soils and nitrate isotopes indicate nitrate is largely derived from natural sources in the Mancos Shale and alluvial material. Thus, in contrast to areas that receive substantial NO₃ inputs through inorganic fertilizer application, Se mitigation efforts that involve limiting NO₃ application might have little impact on groundwater Se concentrations in the study area. Soluble salts are the primary source of Se to the groundwater system in the study area at-present, but they constitute a small percentage of the total Se content of core material. Sequential extraction results indicate insoluble Se is likely composed of reduced Se in recalcitrant organic matter or discrete selenide phases. Oxidation of reduced Se species that constitute the majority of the Se pool in the study area could be a potential source of Se in the future as soluble salts are progressively depleted.