Data were collected as part of a study to identify sources of E. coli contamination at several beaches located in the Grand Calumet River Areas of Concern, located in northern Indiana on Lake Michigan, as well as in Illinois and Wisconsin on Lake Michigan. Water samples were collected at each site in Indiana three times a week for thirteen weeks and at each site in Illinois and Wisconsin. All samples were analyzed for E. coli bacteria (an indicator bacteria for fecal contamination) and species-specific molecular markers (microbial source tracking, MST), including human, gull, and dog. Presence of MST markers indicates a fecal source at that location associated with the target animal. Field conditions were recorded during each site visit (e.g., including air and water temp, wind speed and direction, rainfall, wave height, currents, observations). Water samples were analyzed in the laboratory for E. coli using defined substrate technology and for MST markers using quantitative polymerase chain reaction (qPCR) methods and also turbidity. Lat_long_v2 file includes information regarding sampling locations and their corresponding latitude and longitudes. The E coli_turbidity_v2 data include E. coli densities and turbidity measurements. Data from the qpcr_v4 file includes results from quantitative polymerase chain reaction (qPCR) method for detection of host-specific microbial source tracking markers. Data from SanitarySurvey includes ambient conditions measured in the field: water and air temperature, current speed and direction (eastward, westward, float method), wind direction and speed, wave height, rainfall, and cloud cover. Data from SanitarySurvey_birds included number of birds (gulls, geese, ducks, cormorants, etc.) counted on the beach and in the water. The PowerWater.pdf is the DNA extraction kits' user manual giving detailed instructions for use.