Technical Abstract: Fecal contamination has been an issue for water quality because fecal coliform bacteria are used as an indicator organism to detect pathogens in water. In order to assess fecal contamination in the Wachusett Reservoir Watershed in Massachusetts, USA, the Soil and Water Assessment Tool (SWAT), a commonly used watershed model was used. The SWAT had been augmented with the bacterial fate and transport subroutine, where bacteria die-off is the only in-stream process, and the bacteria module was modified in this study to include solar radiation-associated die-off and the contribution of wildlife. The Latin-Hypercube one at a time (LH-OAT) was used for the sensitivity analysis of hydrologic and modified bacteria modules in the SWAT model. The result demonstrates that solar radiation is one of the most significant fate factors of fecal coliform. A water temperature associated function was added to consider the contribution of beaver activity to fecal contamination in the watershed, resulting in improved prediction accuracy. The modified SWAT model provides an improved estimate of bacteria from the watershed. Our approach will be useful for simulating bacterial concentrations to provide predictive and reliable information of fecal contamination thus facilitating the implementation of effective watershed management.