Recreational water quality monitoring of fecal indicator bacteria (FIB), such as E. coli and Enterococcus sp., currently relies on culture methods that require at least 18 hours for results. Given the short duration of many contamination events, regulatory agencies have demanded rapid methods for more accurate protection of public health. Recently, much work has focused on developing QPCR assays for FIB. Work presented examines the relationships between QPCR- and culture-based assays for FIB in recreational water from several perspectives. Equivalency was compared between culture- and QPCR-measurements of Enterococcus sp. concentrations in beach water samples collected over two summers at two popular southern California beaches. QPCR- and culture-based concentrations were significantly correlated, and management decisions based on the two agreed up to 75% of the time. Persistence of DNA, the QPCR-measured endpoint, versus metabolically active cells, the endpoint of culture-based methods, was tested in seawater mesocosms inoculated with fecal material. QPCR and culture-based measurements conducted in replicate over time revealed that the DNA and cell signals were found to decay at similar rates with few and short-lived significant differences, helping to alleviate concerns that extended DNA persistence may lead to overestimations of FIB concentrations. Additional work was conducted to assess the use of a new QPCR assay to quantify the difficult to culture alternate marker of fecal contamination, fecal Bacteroides spp. The efficacy of the fecal Bacteroides spp. QPCR assay was compared to cultured FIB in lab-created samples and ambient (stormwater) samples. QPCR-measured fecal Bacteroides spp. concentrations were found to be as strongly correlated with contamination by sewage influent as current FIB. Findings also suggest that fecal Bacteroides spp. concentrations may be useful in distinguishing human from animal fecal contamination. Overall, results demonstrate the promise of QPCR-based methods as an improved tool for water quality monitoring. However, technical hurdles remain before QPCR-based monitoring can be implemented. The most important of these is sample processing to remove QPCR-inhibitory compounds. Across this set of studies, approximately 30% of samples experienced some level of inhibition. QPCR should prove a useful tool for water quality management with the advent of standardized approaches for addressing inhibition.