The Newport River Estuary (NPRE), an important North Carolina (NC) shellfish harvesting area, has been experiencing alterations to the land-water interface due to increasing population and coastal development. Water quality degradation in the estuary over the last decade has led to an increase of shellfish harvesting area closures, and has been postulated to be due to non-point source contamination in the form of stormwater. Water samples were taken in the NPRE (n=179) over a range of weather conditions and all seasons from August 2004 to September 2006. Fecal coliform (FC), as estimated by E. coli (EC), and Enterococcus (ENT) concentrations (MPN per 100 ml) were examined in relation to rainfall levels and distance from land. The relationships among the fecal indicator bacteria (FIB) and environmental parameters were also examined. The data revealed a significant increase in FC concentrations after measured rainfall amounts of 2.54 cm (general threshold) and 3.81 cm (management action threshold). However, higher than expected FIB concentrations existed during conditions of negligible rainfall (<0.25 cm), indicating a possible reservoir population in the sediment. Overall, stormwater runoff appears to be adversely impacting water quality in the NPRE.