In May of 2007, a study was initiated by the National Institute of Oceanography (NIO), Goa, India, to investigate the influence of monsoonal rainfall on hydrographic conditions in the Mandovi River of India. The study was undertaken at a location ∼2 km upstream of the mouth of this estuary. During the premonsoon (PreM) in May, when circulation in the estuary was dominated by tidal activity, phytoplankton communities in the high saline (35–37 psu) waters at the study site were largely made up of the coastal neritic species Fragilaria oceanica, Ditylum brightwellii and Trichodesmium erythraeum. During the later part of the intermonsoon (InterM) phase, an abrupt decline in salinity led to a surge in phytoplankton biomass (Chlorophyll 𝑎 ∼14 mg m⁻³), of a population that was dominated by Thalassiosira eccentricus. As the southwest monsoon (SWM) progressed and the estuary freshened salinity and Chlorophyll 𝑎 (Chl 𝑎) concentrations decreased during the MoN, Skeletonema costatum established itself as the dominant form. Despite the low biomass (Chl 𝑎 > 2 mg m⁻³), the phytoplankton community of the MoN was the most diverse of the entire study. During the postmonsoon (PostM), the increase in salinity was marked by a surge in dinoflagellate populations comprising of Ceratium furca, Akashiwo sanguinea, and Pyrophacus horologium.