Urban stormwater runoff in North America is a major source of contamination of surface water bodies. In many parts of the North America, there are combined sewer overflows (CSOs) that are part of aging urban infrastructure. The consequence of these overflows is the discharge of untreated sewage into waterways. In 2001 the US EPA estimated that between 1.8 and 3.5 million people become sick annually due to recreational contact with waters contaminated by sewer overflows. In order for us to have sustainable cities, the challenges of urban stormwater runoff, particularly during extreme events need to be addressed. The goals of our current research are to a) collect baseline data on the concentration of pathogens found in urban waterways, 2) provide evidence based recommendations for the reduction of stormwater runoff using green stormwater infrastructure to ultimately protect public health, particularly vulnerable populations that recreate in these waterways and 3) propose alternative microbial water quality indicators to enable the monitoring of pathogens in these waterways, 4) Perform health based risk assessment to predict the risk of illness associated with recreation in CSO impacted waterways.