Climate change-driven alterations to marine biogeochemistry will impact the formation and trophic transfer of the bioaccumulative neurotoxin methylmercury (MeHg) in the global ocean. We use a 3D model to examine how MeHg might respond to changes in primary production and plankton community driven by ocean acidification and alterations in physical factors (e.g., ocean temperature, circulation). Productivity changes lead to significant increases in seawater MeHg in the polar oceans and a decrease in the North Atlantic Ocean. Phytoplankton MeHg may increase at high latitudes and decrease in lower latitudes due to shifts in community structure. Ocean acidification might enhance phytoplankton MeHg uptake by promoting the growth of a small species that efficiently accumulate MeHg. Non-linearities in the food web structure lead to differing magnitudes of zooplankton MeHg changes relative to those for phytoplankton. Climate-driven shifts in marine biogeochemistry thus need to be considered when evaluating future trajectories in biological MeHg concentrations.