Data were collected to evaluate the efficacy of quantitative polymerase chain reaction (qPCR) as a rapid, alternative method for monitoring recreational water at select beaches and rivers of Sleeping Bear Dunes National Lakeshore (SLBE), in Empire, Michigan. Water samples were collected between August 4 and September 18, 2014 (N=297) from four locations (Esch Rd, Otter Creek, Platte Bay, and Platte River). The samples were analyzed for indicator bacteria, E. coli and enterococci, by both culture-based (membrane filtration, MF; traditional method) and non-culture based (qPCR; rapid method). Recreational water quality standards (RWQS) and beach action values (BAV) were used as indices to compare water quality standard exceedances for MF and qPCR methods; for enterococci: 70 colony-forming units (MF) and 1,000 calibrator cell equivalents and for E. coli: 235 colony-forming units (MF); currently, there are no established RWQS based for qPCR (i.e., CCE) results. The CultureBasedData data include E. coli and enterococci culture-based bacterial counts. Data from the qpcr_v3 file includes results from quantitative polymerase chain reaction (qPCR) method for estimation of E. coli and enterococci counts by DNA-based methods. The Lat_Long file includes information regarding sampling sites at each of the four locations and their corresponding latitude and longitudes.