Metal contamination from base metal sulphide mines is a major environmental challenge that poses many ecological and health risks. We examined the metal concentrations in the Dabaoshan mine in South China in water, sediments, and aquatic organisms and their specific characteristics (i.e. size, body tissue, species, and habitat) along the Hengshi and Wengjiang River courses to assess acid mine drainage remediation efforts. Metal concentrations of arsenic, cadmium, chromium, copper, lead, nickel, thallium, and zinc were examined in tissues (i.e. gills, intestines, and muscles) of 17 freshwater species of fish, shrimps, and crabs. Metals in tissues followed the trend: intestines > gills > muscles; nearly all intestine samples exceeded the safe limits of metals analysed in this study. There is a positive correlation between distance from the mine and metal concentrations related to the flow of surface water and the habitat of aquatic organisms. The concentrations of arsenic, copper, and zinc were the highest in aquatic organisms, and the distribution was influenced by physical (distance from mine, currents, and seasonality), chemical (pH and competing ions), and biological (species, habitat, and predator–prey relation) factors. Large demersal fish and benthic fauna had higher concentrations of metals. Bioaccumulation and biomagnification of metals, as well as the high metal pollution index and target hazard quotient (arsenic, cadmium, copper, lead, thallium, and zinc), occurred in bottom feeders (C. aumtus, X. argentea) and fish belonging to higher trophic levels (P. fulvidraco, O. mossambicus). Lead and cadmium indicated the highest level of biomagnification from prey to predator. Health risks exist from the dietary intake of common aquatic species such as tilapia and carp besides crustaceans due to high arsenic, cadmium, lead, and thallium levels. Further reduction of metals is necessary to improve the effects of acid mine drainage in the catchment.