A mass balance model of mercury (Hg) cycling and bioaccumulation was applied to the Gulf of Mexico (Gulf), coupled with outputs from hydrodynamic and atmospheric Hg deposition models. The dominant overall source of Hg to the Gulf is the Atlantic Ocean. Gulf waters do not mix fully however, resulting in predicted spatial differences in the relative importance of external Hg sources to Hg levels in water, sediments and biota. Direct atmospheric Hg deposition, riverine inputs, and Atlantic inputs were each predicted to be the most important source of Hg to at least one of the modeled regions in the Gulf. While incomplete, mixing of Gulf waters is predicted to be sufficient that fish Hg levels in any given location are affected by Hg entering other regions of the Gulf. This suggests that a Gulf-wide approach is warranted to reduce Hg loading and elevated Hg concentrations currently observed in some fish species. Basic data to characterize Hg concentrations and cycling in the Gulf are lacking but needed to adequately understand the relationship between Hg sources and fish Hg concentrations.