We applied the approach of Kildare et al. to quantitatively detect the source of fecal contamination in several streams in Frederick County. Water samples were collected from the streams within 24 hours following a 0.5+ inch rain storm (“wet samples”) and from the same location when there was no recent prior rain (“dry samples”). This approach uses quantitative polymerase chain reaction (qPCR) to determine the presence of DNA sequences in the water specific to bacteria of the order Bacteroidales that reside in either human or ruminant stool. In addition, we determined the total amount of fecal contamination in each sample with a universal qPCR assay that detects fecal Bacteroidales DNA from any animal source.