A study of pathogen indicators (fecal coliform bacteria) in Onondaga Creek was conducted by the Onondaga Environmental Institute (OEI) in 2007. Data from this study, as well as routine monitoring conducted by Onondaga County as part of its Ambient Monioting Program (AMP), indicated that there were sources of bacteria to Onondaga Creek and Harbor Brook during periods of dry weather. Thus, precipitation-driven discharges of combined sewer outfalls (CSOs) or storm water outfalls did not account for the elevated levels of bacteria frequently observed in both streams.

OEI and county data also showed that bacteria abundance in rural sections of Onondaga Creek is generally high (e.g. 20,000 colonies/ 100 mL) during storms, and can exceed 100,000 colonies/100 mL at downstream, urban sites.

The USEPA, Region II, and NYS Dept of Environmental Conservation (NYSDEC), as well as other members of the Onondaga Lake Partnership (OLP) recognized the need to locate and identify sources of bacteria to both Onondaga Creek and Harbor Brook. Funding was procured to undertake a “Phase I Microbial Trackdown Study” in these two waterways. The emphasis of this study was to monitor the spatial and temporal trends of bacteria; to locate and characterize potential dry-weather bacteria sources. The study was to be undertaken as a joint project of OEI and the Onondaga County Department of Water Environment Protection (OCDWEP), with OEI as the lead agency.