The USGS Water Microbiology Laboratory in Columbus has been working with numerous agencies and USGS Water Science Centers to analyze water samples for microbial source tracking (MST) markers using the quantitative polymerase chain reaction (qPCR) method. Results from MST analyses help to characterize the effects of various sources of fecal contamination in a watershed. Currently, water samples can be analyzed for DNA markers that are associated with humans, cows and other ruminants, dogs, and waterfowl. In addition to MST marker analyses, other steps are generally taken as part of a multi-tiered approach to source tracking. These steps include conducting sanitary surveys, determining the distributions of bacterial indicators in the watershed, and understanding how hydrologic and meteorological processes affect the distributions of indicators and MST markers.