ABSTRACT Tropical cyclones are increasingly affecting estuarine communities. The effects of category-5 tropical cyclone Amphan (landfall on 20 May 2020 near the Ganges estuary mouth) on the copepod community of the Ganges estuary were studied. Copepod assemblages were sampled before (February–December 2019), shortly after (31 May–12 June 2020) and post-(September–November 2020) Amphan periods. It was hypothesized that shortly after Amphan a relatively homogeneous community consisting of a few estuarine specialists would succeed but that would soon be replaced by a heterogeneous one; however, those specialists would continue their dominance. Shortly after Amphan species richness declined but the recovery process was completed within months, led by Paracalanus parvus, Bestiolina similis, Acartia spinicauda, Acartiella tortaniformis and Oithona brevicornis. Spatial homogeneity of the community that prevailed in pre- and shortly after Amphan was lost in post-Amphan. The unilateral dominance of B. similis observed in the pre-Amphan period was challenged by P. parvus, A. spinicauda, A. tortaniformis and O. brevicornis after Amphan. Shortly after Amphan A. spinicauda proliferated and co-dominated the estuary with A. tortaniformis but the latter replaced the former within a few months. The copepod community experienced rearrangements in species composition, abundance and dominance hierarchy; therefore, its regular monitoring is recommended.