Distribution pattern of 58 macrozoobenthic species comprising of polychaetes (10 species) and molluscs (48 species) collected for a period of 2 years from seven selected sites of Hugli estuary and one site of Matla estuary was analyzed in relation to salinity gradients. Out of these 58 species, 21 macrozoobenthic species responded strongly to high salinity (18–33.5‰), 15 species showed salinity tolerance range of 5.1–9.5‰ and 17 species were confined to freshwater sector of Hugli estuary. The remaining five species showed wider range of tolerance to salinity (0.5–33.5‰). The variation in spatio-temporal distribution of macrozoobenthos in the Hugli-Matla estuaries is regulated by the fluctuating salinity along with associated substrate condition and anthropogenic stresses of the sites in the estuaries.