The data being released were part of a project funded by the Great Lakes Restoration Initiative (GLRI). This study sought to examine the influence of filter pore size (5.0 µm pre and 0.22 µm final filtration) on microbial communities and source-specific microbial source tracking (MST) markers at three locations along southern Lake Michigan: Racine, WI; Chicago, IL; and East Chicago, IN; between 2015 and 2017. In 2015, triplicate water samples were collected during three events, in 2016 individual water samples were collected during three events, and in 2017, individual water samples were collected one day a week for ten weeks between June and August. Samples were collected from twelve locations, two river, two river mouth, three offshore, one wetland outlet, and four shorelines. The upstream river locations are as follows: 1. Root River at the Root River Environmental Education Community Center (REC, 2015-2017), Racine, Wisconsin 2. Grand Calumet River at Columbus Drive (GC, 2015-2017), East Chicago, Indiana The river mouth locations are as follows: 1. Grand Calumet River Mouth (GCM, 2015 only), East Chicago, Indiana 2. Root River Mouth (RRM), Racine, Wisconsin The offshore locations are as follows: 1. Grand Calumet River (GCN, 2015 only), East Chicago, Indiana 2. Grand Calumet River (GCE, 2015 only), East Chicago, Indiana 3. Root River marina harbor wall (NBW, 2015 only), Racine, Wisconsin The shoreline locations are as follows: 1. North Beach (NB), Racine, Wisconsin 2. 63rd Street Beach (63rd), Chicago, Illinois 3. Jeorse Park (JP), East Chicago, Indiana 4. Whihala beach (WHW, 2015 only), Whiting, IN The wetland outlet location: 1. North Beach (IEB outlet, 2015 only), Racine, Wisconsin