Starting in 1971, stream flow and climatologic data have been collected in the Goodwater Creek Experimental Watershed, which is part of the Central Mississippi River Basin (CMRB) Long-Term Agroecosystem Research (LTAR) site. Since 1992, water quality and socio-economic data have complemented these data sets. Previous modeling efforts highlighted the challenges created by the presence of a claypan. Specific changes were introduced in the Soil and Water Assessment Tool (SWAT) (i) to better simulate percolation through and saturation above the claypan and (ii) to simulate the spatial and temporal distributions of the timing of field operations throughout the watershed. Our objectives were to document the changes introduced into the code, demonstrate that these changes improved simulation results, describe the model's parameterization, calibration, and validation, and assess atrazine [6-chloro-N-ethyl-N¢-(1-methylethyl)-1,3,5-triazine-2,4-diamine] management practices in the hydrologic context of claypan soils. Model calibration was achieved for 1993 to 2010 at a daily time step for flow and at a monthly time step for water quality constituents. The new percolation routines ensured correct balance between surface runoff and groundwater. The temporal heterogeneity of atrazine application ensured the correct frequency of daily atrazine loads. Atrazine incorporation by field cultivation resulted in a 17% simulated reduction in atrazine load without a significant increase in sediment yields. Reduced atrazine rates produced proportional reductions in simulated atrazine transport. The model can be used to estimate the impact of other drivers, e.g., changing aspects of climate, land use, cropping systems, tillage, or management practices, in this context.