The present study examined the effect of a catastrophic cyclone (Aila) on ichthyofaunal assemblages in a tidal river of the Sundarban Delta. Sampling in six stations with a gill-net of 20-m length and 1-cm mesh size resulted in the collection of 63 species in a pre-Aila survey. Among them, 16 species were not available in the year after the cyclone. However, 12 new species were added to the assemblages in the post-Aila year during which 59 species were recorded. Analysis of Similarity (ANOSIM) confirmed significant changes in fish assemblages after the cyclone with a corresponding reduction of the species diversity and variation in the seasonal pattern of abundance. Hydrological parameters also differed with a significant surge in nutrient concentrations. Tolerance to low dissolved oxygen seemed to be a determinant factor as evident from the higher abundance of certain fishes viz. Harpadon nehereus, Liza parsia, Pampus argentius, Tenualosa ilisha and Toxotes chatareus during post-Aila year. Despite the recovery of the ichthyofaunal assemblages at the later stage of the study, a strong seasonal variation was persistent. The study therefore suggests that environmental variation in terms of increasing temperature and salinity elicit greater response in an estuarine community than temporary natural disturbances even as severe as cyclones.