Inland watersheds in the Southeastern United States are transitioning from agriculture and forested land uses to urban and exurban uses at a rate greater than the national average. This study sampled creeks representing a variety of land use factors in the rapidly urbanizing Jordan Lake watershed. Samples were collected bimonthly under dry-weather conditions and four times during each of three storm events and assessed for traditional microbial indicators of water quality. Fecal indicator bacteria (FIB) concentrations were generally higher in more developed watersheds. FIB concentrations were significantly greater during storm events than during dry-weather conditions, although concentrations demonstrated both intra and inter-storm variability. These results indicate that the magnitude of microbial contamination is influenced by intensity of watershed development, streamflow and antecedent precipitation. Dry-weather FIB loads showed considerable seasonal variation, but the average storm event delivered contaminant loads equivalent to months of dry-weather loading. Analysis of intra-storm loading patterns provided little evidence to support first-flush loading of either FIB. These findings could potentially inform watershed management and public health decisions related to the urbanization of watersheds serving as municipal sources of drinking water.