Microbial pollution in rural streams is a growing concern facing several communities in Ontario. Consequently, watershed managers require sophisticated tools in order to effectively and efficiently meet water quality objectives to ensure the long-term health of their watersheds. This research project investigated the water quality of two small rural watersheds in southwestern Ontario through a comprehensive field monitoring program and the application of water quality modeling. Objectives of this research included the development of a time-series water quality database and the evaluation of the Soil and Water Assessment Tool (SWAT) in modeling microbial pollution. Results from the study show elevated levels of 'E.coli' in both watersheds. In addition, the SWAT computer model was generally able to predict levels of microbial pollution to within an order of magnitude of the observed values. However, it is evident that further research is required to further the development of the latest water quality models.