The field of molecular fecal source tracking in the water environment has developed rapidly since the first PCR assays for general and host-­‐specific Bacteroides 16s rRNA markers were published. Numerous host-­‐specific molecular markers and PCR assays have been developed, adding greater specificity, sensitivity and quantitative methods to the array of options. The public demand for readying methods for transfer to the commercial lab, so that they may be used to generate data for public utilities, citizen action groups and regulatory agencies, has fueled the development of an entire new research community. These methods, however plentiful, have not found community agreement and there is no consensus concerning the appropriate implementation of molecular fecal source tracking in the field. Some issues plaguing the implementation include imperfect marker specificity, environmental variability, DNA extraction variability, PCR inhibition and high cost of molecular analysis. This thesis presents an approach for locating hot spots of human fecal pollution in an urban watershed by using published methodologies for the collection of molecular fecal source tracking data along with a tiered watershed screening tool for cost reduction and two data normalization techniques which ameliorate several known sources of error and strengthen the efficacy of watershed application.