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The sensitivity of the Soil and Water Assessment Tool (2005) and its input parameters that impact the prediction of fecal bacteria concentrations were evaluated. The model was applied at Rock Creek watershed (77 km2), Kansas. Fecal bacteria sources were characterized to use commonly available data to describe model inputs of watershed sources of livestock, septic and wildlife loads. The flow and bacteria loads were validated reasonably for the watershed. The runoff events of the simulated period geometric mean value of the fecal coliform bacteria concentration were evaluated using a relative sensitivity index (S). The four model parameters and one input parameter were tested using Latin Hypercube Sampling (LHS) and independent parameter perturbation (IPP) methods. The model parameters showed no to very high sensitivity (S up to 8.69) and an input parameter determined no to moderate sensitivity (S up to 1.05). If the model is to be used to predict fecal coliform bacteria concentration, particular attention should be taken in characterizing sources and selection of input parameter values.