Beach managers must balance the significant risks of human disease with the social and economic costs of closing public beaches and labeling surface waters as unsafe. Though beaches are closed when fecal indicator bacteria (FIB) concentrations are elevated FIB themselves are not generally pathogenic and estimate the risk of waterborne pathogens. Effective and accurate quantitative microbial risk assessment (QMRA) requires direct measurements of pathogens. Direct measurement of waterborne pathogens has been historically difficult due to cost, labor-intensive methodologies, low concentrations in the environment and problems identifying the correct pathogen(s) to monitor at a given locale. There is need for an affordable and rapid technique to simultaneously determine presence and concentration of myriad waterborne pathogens. Such a tool will be useful to benchmarking which pathogens are posing the greatest risk in recreational waters. We recently designed and partially validated a Pathogen Panel using the high-throughput real-time PCR platform, OpenArray (Life Technologies). OpenArray has been used as a cost-effective diagnostic tool in medical settings (3) but not yet applied to water quality monitoring. Using the Panel we can simultaneously process 64 single-plex nanoscale assays for up to 48 unique samples on a small array card. The high-throughput PCR assay that we have developed and propose to deploy in this work quantifies molecular targets from viral, bacterial and protozoal diarrheal pathogens in triplicate. Additionally, the Pathogen Panel contains targets for general and source specific fecal indicators (human, cow, poultry)- giving the assay broad utility not only for pathogen monitoring and risk assessment but also for determine the source of pollution – which is a key step towards restoration efforts in locations with chronic water quality problems. The research relates directly to the Hudson River Estuary Program’s 2015-2020 Action Agenda in the benefit areas of “Clean Water” and “Education, River Access, Recreation, and Inspiration”.