Escherichia coli distribution and persistence in nearshore Lake Michigan were assessed following heavy rains and sanitary sewer overflow (SSO) and combined sewer overflow (CSO) events over a 5-year period, including an 18-day period following 25.4 cm of rainfall in which intensive studies were conducted following multiple CSO and SSO events. E. coli levels in the Milwaukee estuary and harbor following SSO and CSO events ranged from 10 =4 to nearly 105 CFU/100 mL, which were significantly higher (p ≤ 0.05) than levels following rainfall alone. Sites outside of the breakwall but within the contamination plume (e.g., within 2 km of the harbor) were an order of magnitude lower. Locations 2–5 km from the harbor ranged from below detection limits, of < 1 to 5 CFU/100 mL. E. coli levels corrected for dilution based on specific conductivity measurements were lower than what would be expected for loss due to dilution alone, suggesting a combination of die-off and dilution, were responsible for the rapid disappearance of these organisms outside of the harbor. E. coli and fecal coliforms measured concurrently demonstrated that fecal coliforms could be recovered longer than E. coli in the open waters of the lake. E. coli isolated directly from sewage treatment plant influent were found to have a marked increase in antibiotic resistance traits for ten antibiotics commonly used in the human population compared with isolates from two animal sources of fecal pollution. However, E. coli obtained from sewage impacted water (n = 2,513) and from stormwater impacted water (n = 1,465) collected the previous year when there were no sewage overflows, were found to have no significant difference (p < 0.05) in the frequency of resistance when comparing the two conditions. E. coli survival characteristics and population dynamics are most likely influenced by multiple factors in complex systems such as the watershed/estuarine/lake environments of the Great Lakes.