This paper presents a developing tool to aid in watershed protection called microbial source tracking (MST). MST can be used to provide the scientific basis for identifying microbial input sources to raw drinking water. Once a source is identified by MST methods, a water utility can develop and implement effective remedial actions in a targeted manner without spending money and effort on "false" sources that may be indicated through land use analysis or sanitary surveys alone. Many MST tools involve molecular analyses; however, this study focused on tools which could be more easily and less expensively implemented by watershed managers. An integrated assessment approach was applied to two watershed "hotspots." Sites were selected based on elevated fecal coliform counts enumerated during monitoring for regulatory compliance. Land use analysis was used to identify the potential microbial contamination sources, which included residential septic systems, agricultural animal operations, commercial/industrial operations and wildlife activity. Water samples were collected seasonally at each site and analyzed for a suite of water quality parameters. The MST methods employed included sorbitol-fermenting Bifidobacteria and enterococci (indicators of human-related domestic wastewater), Rhodococcus coprophilus (an indicator of grazing animal waste), and male-specific RNA coliphage serotypes (that discriminate between human and non-human microbial inputs). Traditional water quality parameters were also measured to assess the general extent of contamination. These included conductivity, turbidity and fecal coliforms. Includes tables.