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. The study was funded by the Great Lakes Restoration Initiative. Water samples were collected at each site (Jeorse Park 1, Jeorse Park 2, Hammond East, Hammond West, Whihala West, Whihala East, Whihala west breakwater, Hammond Marina, Whihala offshore locations, and the Grand Calumet River) one day a week or three times a week between 2015 and 2018. While the 2015 data were included in analysis, these data were previously publicly released https://doi.org/10.5066/F7H70F3D. Samples (water, sand, sediment) were analyzed for E. coli bacteria (an indicator bacterium for fecal contamination) and species-specific molecular markers (microbial source tracking, MST), including human (HF183, Mnif), gull (Gull2), and dog (DogBact). Presence of MST markers indicates a fecal source associated with the target animal at that location. Bird counts were recorded during each site visit. Water samples were analyzed in the laboratory for E. coli using defined substrate technology, for MST markers using quantitative polymerase chain reaction (qPCR) methods, and turbidity, conductivity, and pH. Additionally in 2015, samples were collected during two dry and one wet event and subjected to metagenomics analysis for determining bacterial communities. The additional samples were collected at Whihala, Jeorse Park, Grand Calumet River, as well as three offshore locations associated with the Grand Calumet River: mouth to the lake at a peninsular structure and north and east of the structure. Lat_long file includes information regarding sampling locations and their corresponding latitude and longitudes. The EcoliWaterChem data include E. coli densities and water chemistry (turbidity, conductivity, pH) measurements. Data from the MST file includes results from quantitative polymerase chain reaction (qPCR) method for detection of host-specific microbial source tracking markers as follows: Gulls (Gull2), Dogs (DogBact), and human (HF183, Mnif). Data from Birds included number of birds (gulls, geese, ducks, cormorants, etc.) counted on the beach and in the water. The metagenomics file includes taxonomic information and corresponding percent abundance of each organism for each sample. The metagenomics file includes taxonomic information and corresponding organisms' percent abundance for each sample. The metagenomicsKey file includes information pertinent to individual samples.