Changes in the phytoplankton biomass (chlorophyll a), production rate, and species composition were studied over two seasons using the time series measurements in the northern limb of the Cochin estuary in relation to the prevailing hydrological conditions. The present study showed the significant seasonal variation in water temperature (F=69.4, P<0.01), salinity (F=341.93, P<0.01), dissolved inorganic phosphorous (F=17.71, P<0.01), and silica (F=898.1, P<0.01) compared to nitrogen (F=1.646, P>0.05). The uneven input of ammonia (3.4-224.8 μM) from upstream (Periyar River) leads to the inconsistency in the N/P ratio (range 6.8-262). A distinct seasonality was observed in Si/N (F=382.9, P<0.01) and Si/P (F=290.3, P<0.01) ratios compared to the N/P ratio (F=1.646, P>0.05). The substantial increase in chlorophyll a (average, 34.8±10 mg m(-3)) and primary production (average, 1,304±694 mg C m(-3) day(-1)) indicated the mesotrophic condition of the study area during the premonsoon (PRM) and it was attributed to the large increase in the population of nanoplankton (size<20 μ) such as Skeletonema costatum, Thalassiosira subtilis, Nitzschia closterium, and Navicula directa. In contrast, during the post monsoon (PM), low chlorophyll a concentration (average, 9.3±9.2 mg m(-3)) and primary production (average, 124±219 mg C m(-3) day(-1)) showed heterotrophic condition. It can be stated that favorable environmental conditions (optimum nutrients and light intensity) prevailing during the PRM have enhanced the abundance of the nanoplankton community in the estuary, whereas during the PM, the light limitation due to high turbidity can reduce the nanoplankton growth and abundance, even though high nutrient level exists.