In New York State, 792 waterbodies are on the “Impaired/TMDL” list, which identifies bodies of water that might require remediation. The Sparkill Creek, placed on the list first in 2010, empties into the Hudson River. It faces issues with stormwater runoff, causing elevated levels of pathogens in the creek and decreased oxygen availability. According to published data, the levels of the indicator bacteria are 24 times higher than EPA standards. The Pocantico River, located in Westchester County, faces many of these same issues. Both were tested for microbial and coliphage loads and diversity as related to weather events. Coliform and E. coli levels were measured, with a significant increase found with a rainfall event for both sampling locations. The coliphage numbers and diversity were also significantly different with a rain event. Microbial community analyses were also completed. Of note was increased prevalence of Enterobacter and Escherichia three miles from the mouth of the creek. Future studies include a more thorough analysis of the microbial community data in both time and space, along with further testing of the fungal, bacterial, and algal populations.