Phytoplankton cell numbers and chlorophylla determinations were made during the premonsoon, monsoon and postmonsoon periods in the Mandovi-Zuari estuarine complex (west coast of India). Primary productivity estimates agreed well with chlorophylla and phytoplankton cell numbers. The consequent decline in salinity with the onset of monsoon was found to be an important factor controlling the distribution, abundance and productivity of phytoplankton. As compared to the Zuari estuary, the Mandovi retained typical estuarine conditions and a greater phytoplankton biomass. Based on primary productivity estimations, the potential fishery resource of this estuarine complex has been computed.