The validation of rapid analytical methods, such as qPCR, in the context of monitoring schemes for detection and enumeration of fecal indicator bacteria in aqueous environments are necessary prior to implementation. In Racine, WI, composite sample analysis via a culture-based assay is routinely utilized for regulatory decisions regarding bathing water quality. The objective of this study was twofold: 1) to determine if composite sample values would fall within the range of three or four individual values when quantifying E. coli using qPCR and 2) conclude whether similar regulatory decisions would be made based on a molecular method (using the 1986 US EPA Ambient Water Quality guidelines for fresh water). During the 2009 (9 events) and 2010 (11 events) bathing seasons individual (North Beach = 4; Zoo Beach = 3) and composite samples were analyzed using both a culture-based (IDEXX) and molecular method. Composite values almost always fell within the range of the three or four individual sample values (IDEXX = 95% and qPCR = 80 - 90%). In every instance save one, when E. coli levels exceeded US EPA primary contact usage guidelines, the composite value fell within the range of the beaches' individual sites and was equivalent to both daily arithmetic and geometric mean values. This data shows that compositing of samples could continue at these two freshwater beaches when employing qPCR and that the use of molecular methods would result in similar regulatory action (80% agreement). More rapid notification is desirable while maintaining costs and adequate spatial characterization.