The molecular sewage indicator, coprostanol, was measured in bed sediments of the Mississippi River for the purpose of determining sewage contamination. Coprostanol is a non-ionic, non-polar, organic molecule that associates with sediments in surface waters, and concentrations of coprostanol in bed sediments provide an indication of long-term sewage loads. Because coprostanol concentrations are dependent on particle size and percent organic carbon, a ratio between coprostanol (sewage sources) and cholestanol + cholesterol (sewage and non-sewage sources) was used to remove the biases related to particle size and percent organic carbon. The dynamics of contaminant transport in the Upper Mississippi River are influenced by both hydrologic and geochemical parameters. A mass balance model incorporating environmental parameters such as river and tributary discharge, suspended sediment concentration, fraction of organic carbon, sedimentation rates, municipal discharges and coprostanol decay rates was developed that describes coprostanol concentrations and therefore, expected patterns of municipal sewage effects on the Upper Mississippi River. Comparison of the computed and the measured coprostanol concentrations provides insight into the complex hydrologic and geochemical processes of contaminant transport and the ability to link measured chemical concentrations with hydrologic characteristics of the Mississippi River.