Research on mercury (Hg) in aquatic ecosystems in China has focused mainly on fish, with little research on the base of the food chain and Hg bioaccumulation mechanisms. This paper summarizes research progress pertaining to the characteristics, current status, and trends of Hg accumulation in the aquatic food chain in China, analyzes the effects of human activities on the transmission and accumulation of Hg in aquatic food chains, and assesses their risks to human and ecosystem health. A comparison of fish samples in China between 2000 and 2018 indicates that their total Hg content remains at relatively safe levels. However, because current information is generally insufficient to confirm how anthropogenic activities affect transformation and bioaccumulation in the aqueous environment, Hg isotope studies should be a focus of research on aquatic food webs. Additionally, more attention should be paid to Hg transport and bioaccumulation in the basic food chain by focusing on multi-contaminant joint exposure studies and establishing Hg bio-transport models.