The state of Iowa requires developing total maximum daily loads (TMDLs) for over 400 water bodies that are listed on the 303(d) list of the impaired waters. The Raccoon River watershed, which covers approximately 9400 km2 of prime agriculture land and represents a typical Midwestern corn-belt region in west-central Iowa, was found to have three stream segments impaired by nitrate-N. The Soil and Water Assessment Tool (SWAT) was applied to this watershed to facilitate the development of a TMDL. The modeling framework integrates SWAT with supporting software and databases on topography, land use and management, soil, and weather information. Annual and monthly simulated and measured streamflow and nitrate loads were strongly correlated. The watershed response was evaluated for a suite of watershed management scenarios where land use and management changes were made uniformly across the watershed. A scenario of changing the entire land to row crop resulted in an increased nitrate load of about 12% over the baseline condition at the watershed outlet. Results from the 15 nitrate load reduction strategies were found to reduce nitrate from < 1% to about 85%, with the greatest potential reduction associated with changing the row crops to grassland. This research demonstrated the use of a modeling system to facilitate the analyses of TMDL implementation strategies, including the ability to target the most efficient allocation of alternative practices on a subwatershed basis.