This data article includes information on the impact of gold mining along five zones of a tropical river in the Pacific region of Colombia. The concentrations of total mercury (THg), total length, mertimercury (MeHg) were determined in 16 species of fish. With this information, it was shown as the concentrations of mercury in fish are influenced by the distribution in the contamination along the Atrato River Basin [1]. Further, THg and MeHg concentrations were related with the trophic level to show biomagnification, and with total length to show bioaccumulation, which is important to establish the potential risk to the environment and also to the health of the inhabitants living along the basin from the consumption of fish.