Mercury is one of the primary contaminants of global concern. As anthropogenic emissions of mercury are gradually placed under control, evidence is emerging that biotic mercury levels in many aquatic ecosystems are increasingly driven by internal biogeochemical processes, especially in ecosystems that have been undergoing dramatic environmental changes. Here we review the unique properties of mercury that are responsible for the exceptional sensitivity of its biogeochemical cycles to changes in climatic, geochemical, biological and ecological processes. We show that, due to rapid climate warming, a shift from sources-driven to processes-driven mercury bioaccumulation is already happening in the Arctic marine ecosystem. We further suggest that such a shift might also be operating in the Three Gorges Reservoir due to changes in these biogeochemical processes induced by the damming. As a result, the effectiveness of mercury emission control is expected to be followed by long delays before ensuing reduction is seen in food-web levels, making it all the more pressing to control and reduce mercury emissions to the reservoir. Long-term monitoring and targeted studies are urgently needed to understand how biotic mercury levels in the reservoir are responding to changes in mercury emissions and in biogeochemical processes.