The port ecosystems are prone to deterioration due to the maritime and coastal activities and as a major source of the country’s economy need efficient management. Phytoplankton communities can serve as reliable indicators of the prevailing environmental conditions due to their short life cycles. Seasonal sampling was conducted at 26 stations from October 2014 to February 2016 at Kandla port situated in a creek, along the west coast of India. The post-monsoon and monsoon water temperatures were higher (30 °C) whereas pre-monsoon were lower (21 °C). The salinity varied from polyhaline (18–30; monsoon) to euhaline (30 to 45; non-monsoon). The strong currents, high tidal activity, shallow depth areas, and the creek backwater systems make this ecosystem well-mixed and turbid. The annual average trophic index (TRIX) scores indicated very good water quality and low eutrophication, except during pre-monsoon (2.3 ± 0.7 to 4.1 ± 0.2). Based on the cell size, the phytoplankton community was classified into two main groups, i.e., nano-microphytoplankton, which comprised forty-seven species (represented by diatoms, dinoflagellates, and silicoflagellates) and picophytoplankton including two groups (picocyanophytes and picoeukaryotes). The diatoms and picophytoplankton dominated the total biomass and cell abundance, respectively. Only the picophytoplankton exhibited significant seasonal variations in cell abundance and carbon biomass. The lowest monsoon phytoplankton abundance coincided with high turbidity and vice versa during the post-monsoon. The hypersaline pre-monsoon environment with lower annual temperature, relatively lower turbid waters, and increased nutrients favoured higher diatom diversity. These conditions also supported potentially harmful Gymnodinium sp. and bloom-forming Tripos furca and Pyrophacus sp. Overall, ten non-toxic but bloom-forming species were observed. The study provides insights into the phytoplankton community’s response to environmental conditions that can have repercussions on the ecosystem’s functioning.