The ability to accurately simulate flow and nutrient removal in treatment wetlands within an agricultural, watershed-scale model is needed to develop effective plans for meeting nutrient reduction goals associated with protection of drinking water supplies and reduction of the Gulf of Mexico hypoxic zone. The objectives of this study were to incorporate new equations for wetland hydrology and nutrient removal in Soil and Water Assessment Tool (SWAT), compare model performance using original and improved equations, and evaluate the ramifications of errors in watershed and tile drain simulation on prediction of NO3-N dynamics in wetlands. The modified equations produced Nash-Sutcliffe Efficiency values of 0.88 to 0.99 for daily NO3-N load predictions, and percent bias values generally less than 6%. However, statistical improvement over the original equations was marginal and both old and new equations provided accurate simulations. The new equations reduce the model's dependence on detailed monitoring data and hydrologic calibration. Additionally, the modified equations increase SWAT's versatility by incorporating a weir equation and an irreducible nutrient concentration and temperature coefficient. Model improvements enhance the utility of SWAT for simulating flow and nutrients in wetlands and other impoundments, although performance is limited by the accuracy of inflow and NO3-N predictions from the contributing watershed. Editor's note: This paper is part of the featured series on SWAT Applications for Emerging Hydrologic and Water Quality Challenges. See the February 2017 issue for the introduction and background to the series.