Changes in the autotrophic pico- (0.2– 2 μm), nano- (2–20 μm), and microplankton (>20 μm) biomass (chlorophyll a) and primary production were measured in the estuarine and coastal waters off Cochin, southwest coast of India during the onset and establishment of a monsoon. During this period, the estuary was dominated by nutrient-rich freshwater, whereas the coastal waters were characterized with higher salinity values (>30 psu) and less nutrients. The average surface chlorophyll a concentrations and primary production rates were higher in the estuary (average 13.7 mg m−3 and 432 mgC m−3 day−1) as compared to the coastal waters (5.3 mg m−3 and 224 mgC m−3 day−1). The nanoplankton community formed the major fraction of chlorophyll a and primary production, both in the estuary (average 85 ± SD 8.3% and 81.2 ± SD 3.2%) and the coastal waters (average 73.2 ± SD 17.2% and 81.9 ± 15.7%). Nanoplankton had the maximum photosynthetic efficiency in the coastal waters (average 4.8 ± SD 3.9 mgC mgChl a m−3 h−1), whereas in the estuary, the microplankton had higher photosynthetic efficiency (average 7.4 ± 7 mgC mgChl a m−3 h−1). The heavy cloud cover and increased water column turbidity not only limit the growth of large-sized phytoplankton in the Cochin estuary and coastal waters but also support the proliferation of nanoplankton community during the monsoon season, even though large variation in nanoplankton chlorophyll a and production exists between these two areas.