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The taxonomic composition, abundance, diversity and spatial distribution of phytoplankton and zooplankton, as well as the prevailing hydrographic conditions, were examined in the Whin Estuary, which is considered one of the most pristine and productive coastal ecosystems of Ghana, which is located on the Gulf of Guinea. Hydrographic and plankton variables were determined along the gradient of the estuary between March and July 2022 across two seasons and tidal periods. A total of 50 genera of phytoplankton and 27 genera of zooplankton were recorded across the two seasons and sampling periods. Diatoms and copepods dominated the plankton communities across the estuary. Plankton genera such as Navicula, Nitzschia, Thalassiosira, Cyclops, Paracalanus and Temora were recorded across all the seasons and tidal periods, despite the varying hydrographic conditions. The environmental variables varied across the seasons, tidal periods and sampling stations in the estuary. For instance, temperature, DO, transparency, and chlorophyll a varied significantly (p < 0.05) across both the seasons and tidal periods. pH values were significantly (p < 0.05) lower in the rainy season compared to the dry season. There was a strong salinity gradient across the estuary, with the upper reaches dominated by freshwater organisms, such as cladocerans and cyanobacteria, and the lower reaches by marine organisms, primarily diatoms and copepods. In sum, the results reported here are important as they highlight the distribution of plankton communities in a tropical estuarine ecosystem and can serve as a reference for the management of tropical brackish ecosystems. [ABSTRACT FROM AUTHOR]