In this study, two different versions of the Soil and Water Assessment Tool (SWAT) model were used to simulate the hydrology and biogeochemical response of the Cannonsville Reservoir watershed, in New York. The first version distributes overland flow in ways that are consistent with variable source area (VSA) hydrology driven by saturation excess runoff, whereas the second version is the standard version of SWAT. These two models were each calibrated for streamflow (Flow), particulate phosphorus (PP), total dissolved phosphorus (TDP), and sediment (Sed) against measured data from the 1,200 km2 Cannonsville watershed. The standard version of the model yielded an r2 between the measured and simulated data of 0.85, 0.73, 0.70, and 0.72 for Flow, Sed, TDP, and PP, respectively. The VSA version yielded an r2 of 0.84, 0.69, 0.72, and 0.53 for Flow, Sed, TDP, and PP, respectively. The two models were then used to determine the maximum upper bound on the reduction in phosphorus loading by removing all of the corn in the watershed. The average reductions between the two models were 65 and 37% for PP and TDP, respectively. The VSA version was also used to estimate the effect of moving corn land in the watershed from the wettest, most runoff prone areas to the driest, least runoff prone areas, which cannot be done directly with the standard SWAT model.