5-day composite river water samples were collected from two sites: Menomonee River (U.S. Geological Survey station number 04087142) and Underwood Creek (U.S. Geological Survey station number 04087088) in Milwaukee, Wisconsin. 5-day composite wastewater (raw sewage) influent samples were also collected from the Jones Island Water Reclamation Facility (U.S. Geological Survey station number 430125087540400). 5-day composite samples were collected from 2017 to 2019. Grab samples and time-series data (one-hour streamflow and 10-minute optical sensor measurements) were also collected from the Menomonee River (U.S. Geological Survey station number 04087142) site from 2017 to 2018, which are presented in this data release. Both 5-day composite and grab samples were analyzed for absorbance spectra and fluorescence excitation-emission matrices (EEMs), which are also presented in this data release. 5-day composite and grab samples were also analyzed for waterborne pathogens, human-associated and fecal-indicator bacteria, dissolved organic carbon and pharmaceutical compounds, which are archived in the U.S. Geological Survey National Water Information System (NWIS; http://waterdata.usgs.gov/nwis). The data presented in this data release and the data collected and archived in NWIS were used to develop models using ordinary least squares regression (two-single site models) and linear mixed effect models (R package lme4; eight multi-site models) and are presented as a “child item” to this data release. Concentrations of human-associated bacteria and fecal-indicator bacteria were used as response variable. Human-specific bacteria included human bacteroides, and lachnospiraceae. Fecal indicator bacteria included E. coli and enterococci. Turbidity and optical properties of water (various fluorescence and absorbance signals) were used as predictor variables.