Large quantities of contaminants enter Canadian waterways through municipal wastewater effluent (MWWE) each year. MWWE exposure can have a myriad of effects on aquatic organisms, including inducing chronic stress response or altering hormone signaling. A key site for many of these effects is the liver, which controls xenobiotic metabolism, energy regulation, and other functions related to the maintenance of homeostasis. One method for analyzing changes in liver function is shotgun proteomics, which uses mass spectrometry data to identify and quantify proteins in a tissue or sample. The objective of this thesis is to investigate changes in the liver proteome in fathead minnows caged upstream and downstream of wastewater treatment plants (WWTPs) in the Bow River, Alberta.