The aim of this study was to investigate the potential impact of effluent released during metals extraction from polymetallic sea nodules at the Pilot Plant at National Metallurgical Laboratory, India, by analysing different metal (Mn, Cu, Zn, Fe, Pb and Cr) concentrations in six tissues (skin, muscles, gills, liver, kidney and brain) of the fish Labeo rohita. Of the six analysed tissues of sea-nodule-effluent-exposed fish, liver accumulated highest concentration of most of the metals (2.91–287.36 mg kg−1) while muscles (2.1–81.14 mg kg−1) lowest. While the concentration of Fe was maximum (60.41–218.7 mg kg−1) in all the tissue systems (except muscles and liver), Pb was minimum (0.8–2.91 mg kg−1). Accumulation of most of the metals in all the tissues was above the safe limits as recommended by Food and Agricultural Organisation that indicate metal’s potential hazardous impact on the fish. High bioaccumulation factors for these metals in the different tissues revealed that metals were extensively bio accumulated and bio concentrated. The time-dependent variation in metal pollution index illustrated increase in gross metal load (p < 0.05) in different tissue components with increase in exposure period. In conclusion, the sea nodule effluent was found to cause adverse health impact on the fish which in turn might also affect the human health when consumed.