Surface waters within the basin of the Laurentian Great Lakes are impacted by microbial contamination from municipal wastewater and agricultural runoff, as well as from other sources. In particular, microbial contamination of drinking water is an ongoing problem within many Indigenous communities located in the basin. However, it is difficult to identify the sources of microbial contamination using the traditional monitoring approaches with fecal indicator bacteria, such as total coliforms and Escherichia coli (E. coli). In this study, we evaluated whether surface waters in the basin are contaminated with fecal bacteria of human origin using chemical indicators of domestic wastewater (i.e., caffeine and sucralose) and with Bacteroidales 16S rRNA markers. Study areas included the Grand River watershed within the Lake Erie basin and three nearshore locations within the Great Lakes basin. Two of these sites are sources of drinking water for Indigenous communities. We assessed whether there were relationships between the concentrations of fecal indicator microorganisms and chemical indicators of domestic wastewater at selected study locations. Analysis of genetic markers indicated that about 30% of the Bacteroidales bacteria present at a site in the Grand River were of human fecal origin and the balance were of bovine or general animal origin. The presence of caffeine and sucralose in surface waters indicated that there was upstream contamination by domestic wastewater. However, in the drinking water treatment plant operated by Six Nations of the Grand River, the levels of these chemical indicators and fecal bacteria were reduced by the advanced water treatment technologies. The concentrations of sucralose and caffeine collectively were strongly correlated with the levels of total coliforms in samples from the Grand River (R2 = 0.75) and with levels of E. coli in samples from the Great Lakes basin (R2 = 0.97), but there appeared to be an upper threshold for this relationship. These data indicate that analysis of caffeine and sucralose and genetic markers for strains of Bacteroidales fecal bacteria may be useful tools for identifying the sources of microbiological contamination of surface waters and drinking water.