Structural dynamics of the microphytoplankton community in accordance with the seasonal and inter-annual variations were assessed along the Cochin estuary, a tropical backwater in the southwest coast of India. Field observations were carried out for two years (January 2019 to December 2020) on a weekly basis. The study highlights significant variabilities in the community composition of microphytoplankton with respect to the diversity and abundance during the three seasons (pre-monsoon, monsoon, and post-monsoon). However, inter-annual variations were not much prominent. Although diatoms formed the major taxa for the study site in terms of average numerical abundance, a periodic shift between cyanobacteria (pre-monsoon), green algae (monsoon), and dinoflagellates (post-monsoon) was also observed. Blooms of diatoms, dominated by centrales like Skeletonema costatum, Cerataulina bicornis, Leptocylindrus danicus, Chaetoceros spp., and Thalassiosira spp. and by the dinoflagellate Akashiwo sanguinea were common in both the years. However, blooms of Tripos furca, Peridinium quadridentatum, and Noctiluca scintillans were only reported during the year 2020. The present study emphasized that the estuarine phytoplankton community structure varied significantly with variability in the physical parameters like water temperature and salinity, thus leading to the seasonality of phytoplankton composition in these ecosystems.