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Fecal coliform bacteria contamination is one of the causes of water-quality impairments in surface waters which often result from the non-point source pollution, including grazing operations, failing septic system and wildlife. The Soil and Water Assessment Tool (SWAT) microbial sub-model 2005, was used to simulate the daily flows, total suspended solids, and fecal coliform bacteria concentrations in three grazed sub-watersheds (Auburn, Deer Creek, Rock Creek) of the Upper Wakarusa watershed in the northeast Kansas. The watershed characteristics for bacterial source, such as livestock, human, and wildlife, were modeled with four separate combinations to evaluate the source specific bacteria concentration at the outlet of the each watershed using modified deterministic probability of bacteria source tracking data.