Ground and surface water selenium (Se) contamination is problematic throughout the world, leading to harmful impacts on aquatic life, wildlife, livestock, and humans. A groundwater reactive transport model was applied to a regional‐scale irrigated groundwater system in the Lower Arkansas River Basin in southeastern Colorado to identify management practices that remediate Se contamination. The system has levels of surface water and groundwater Se concentrations exceeding the respective chronic standard and guidelines. We evaluate potential solutions by combining the transport model with an assessment of the cost to employ those practices. We use a framework common in economics and engineering fields alike, the Pareto frontier, to show the impact of four different best management practices on the tradeoffs between Se and cost objectives. We then extend that analysis to include institutional constraints that affect the economic feasibility associated with each practice. Results indicate that although water‐reducing strategies have the greatest impact on Se, they are the hardest for farmers to implement given constraints common to western water rights institutions. Therefore, our analysis shows that estimating economic and environmental tradeoffs, as is typically done with a Pareto frontier, will not provide an accurate picture of choices available to farmers where institutional constraints should also be considered.