Large coastal areas have been closed to shellfishing by fecal coliform pollution. Sources of contamination include humans and animals, with conveyance by storm-water runoff an increasingly important problem in rapidly developing coastal areas. Estuarine waters in southwestern Brunswick County, North Carolina, have long been closed to shellfishing, but sources and modes of fecal contamination have been debated. Water-quality monitoring data allowed evaluation of storm-water runoff and malfunctioning septic systems as causes for closures. Fecal coliform concentrations did not respond to changes in salinity. Plots of fecal coliform concentrations vs. rainfall totals in the 48-hour period prior to sampling at 10 monitoring locations in shellfishing waters revealed no clear rainfall effect. There were no significant differences in fecal coliform concentrations between periods with no rainfall in the preceding 72 hours and 24- or 48-hour periods with any rainfall at 9 of 10 monitoring locations. Fecal coliform concentrations after the highest 48-hour rainfalls (>1.5″) were not significantly higher than the highest concentrations after dry periods. Thus, storm-water runoff alone could not account for fecal coliform contamination in these shellfishing waters. The highest fecal coliform concentrations at monitoring locations within the estuarine watersheds were associated with on-site human waste-treatment systems. Site inspections confirmed that some instances of high fecal coliform counts resulted from improperly performing septic systems. Densities of septic systems reached 20/ha, with many areas of high density having soils severely limited for septic-system suitability. Ditching and drainage systems in densely developed areas facilitated septage discharge to adjacent estuarine waters. Although storm water conveyed some of the total load of nonhuman fecal contaminants, it also conveyed fecal contaminants from poorly performing septic systems, which, under these circumstances, represent important sources of fecal contamination.