The present study was undertaken with an aim to estimate the health of marine environment of Kerala in terms of primary production, chlorophyll a and community structure of phytoplankton with respect to existing environmental conditions. Maximum productivity (27.26 mg C m-3 h-1), chlorophyll-a concentration (3.83 mg m-3) and phytoplankton density (5928 cells L–1) were observed at Paravur, where as low productivity, chlorophyll a and phytoplankton count were observed at Veli. Maximum diversity of phytoplankton was encountered at Kasaragod. A total of 29 genera of phytoplankton comprising 23 diatoms, 4 dinoflagellates and each of blue green algae and green algae were identified. The most common diatom encountered in the study was Chaetoceros, Coscinodiscus and Pleurosigma. The acidic effluent discharged from Travancore Titanium Products Limited (TTP) seems to have adversely affected the phytoplankton diversity, abundance and the primary productivity at Veli. Along the Kerala coast, Phytoplankton abundance, community structure and biomass could be controlled by spatial variability of nutrients and species specific association with respect to differences in the hydrographical conditions and anthropogenic inputs from point sources.