Water quality often limits the potential uses of scarce water resources in semiarid and arid regions. To best manage water quality one must understand the sources and sinks of both solutes and water to the river system. Nutrient concentration patterns can identify source and sink locations, but cannot always determine biotic processes that affect nutrient concentrations. Modeling tools can provide insight into these large-scale processes. To address questions about large-scale nitrogen removal in the Middle Rio Grande, NM, we created a system dynamics nitrate model using an existing integrated surface water--groundwater model of the region to evaluate our conceptual models of uptake and denitrification as potential nitrate removal mechanisms. We modeled denitrification in groundwater as a first-order process dependent only on concentration and used a 5% denitrification rate. Uptake was assumed to be proportional to transpiration and was modeled as a percentage of the evapotranspiration calculated within the model multiplied by the nitrate concentration in the water being transpired. We modeled riparian uptake as 90% and agricultural uptake as 50% of the respective evapotranspiration rates.