Selenium (Se) is an essential micro-nutrient for humans and animals but can be toxic at high levels of intake. Quantifying the transport of Se in environmental systems is essential for understanding and mitigating Se contamination in soils, groundwater, and surface waters. In this study, we investigate the transport, storage, and contamination of Se in highly managed, irrigated watershed systems to explore historical conditions, the dominant environmental controls on Se contamination and transport, and the impact of anthropogenic influences such as irrigation and urbanization. We use a portion (23,600 km