Storm events and other periods of high runoff transport large quantities of suspendedorganic, inorganic, chemical, and biological materials into streams when compared to base stream flow conditions. In an effort to evaluate the full impact of storm events on the water quality of the streams feeding the water supply reservoirs, the New York City Department of Environmental Protection (NYCDEP) Pathogen Monitoring Program has been performing storm water monitoring for pathogens since 1993. There is no established sampling methodology designed to characterize pathogen concentrations and loads in streams during storm events. The NYCDEP has developed several unique monitoring protocols and has field-tested them over the last five years to characterize the concentration and load of pathogens during a storm event. In addition to developing protocols, specialized equipment and materials were constructed, improvised, and field tested to facilitate the monitoring. Logistical needs specific to the program have been identified and infrastructure requirements delineated. This paper discusses NYCDEP's Pathogen Monitoring Program storm water monitoring methodology. Includes 28 references, figures.