Monomethylmercury (MMHg) is a toxic and bioaccumulative compound that poses serious health threats to wildlife and humans consuming fish. There are significant uncertainties concerning the MMHg sources and exposure pathways to aquatic food webs and mercury stable isotope studies are beginning to shed new light on these processes. In Chapter 2 and 3, we conducted a series of controlled feeding experiments to understand the behavior of mercury isotopes during bioaccumulation and trophic transfer in freshwater and marine food webs. We found that there is an absence of mercury isotope fractionation during bioaccumulation, trophic transfer, and transport of MMHg between food sources and different tissues within fish. We used this information to develop the application of mercury isotopes as a monitoring tool for identifying MMHg sources in natural environments. In Chapter 4 and 5, we applied mercury isotopes to investigate the MMHg sources and exposure pathways in coastal marine food webs and in lacustrine-terrestrial transition food webs. Our work has elucidated spatial and ecological variability in MMHg sources as well as movements between terrestrial and aquatic ecosystems. This dissertation demonstrates that mercury stable isotopes can enhance our knowledge of the complexities of MMHg sources and biogeochemistry in natural ecosystems.