My dissertation evaluated the prevalence and distribution of legacy and emerging contaminants in food webs of the Laurentian Great Lakes. Although Lake Michigan and its basin were the primary focus of my research, my dissertation is broadly applicable to the Great Lakes watershed and aquatic ecosystems that face similar legacy and emerging contaminant threats. My dissertation demonstrated that contaminant accumulation and distribution within fish is influenced by a variety of ecological factors, including life history strategies, diet, habitat utilization, and size. By combining novel measurement techniques and modeling approaches, I identify important processes controlling the bioaccumulation and biomagnification of mercury, microplastics, and per- and polyfluoroalkyl substances (PFAS) in Lake Michigan fish. First, I demonstrate that mercury bioaccumulates and biomagnifies in six Lake Michigan prey fish and show that differences are due to ontogeny, trophic position, and habitat. Next, I determine that microplastic concentrations and types present in Indiana waterways are influenced by atmospheric deposition rather than land-use. Then, I provide the first evidence of maternal transfer of PFAS to embryos in fish. I then evaluate the differences in PFAS concentration across all major fish tissue types to provide recommendations for tissue types that will enhance cross-study comparisons. I also determine that an iteroparous species (steelhead trout) had higher total body burdens of PFAS compared to semelparous species (Chinook and coho salmon), suggesting that repeat spawners have more opportunities for PFAS exposure and acquisition. Finally, I adapt and optimize a rapid method for measuring total fluorine as a proxy for PFAS using Particle-Induced Gamma-ray Emission (PIGE) spectroscopy, which will increase sample through-put and reduce cost for processing PFAS samples when compared to Liquid Chromatography with tandem Mass Spectroscopy (LC-MS/MS). Overall, my dissertation demonstrates that contaminants display complex interactions with the aquatic environment and within the bodies of organisms. Further, the ecological diversity of fish in reproduction, diet, and habitat utilization influences contaminant exposure, acquisition, and release. A better understanding of how contaminants behave within aquatic ecosystems may help to prevent introduction or with isolating and mitigating contaminants that already exist within the environment.