Even though the seasonal pattern of phytoplankton biomass distribution in the seas around India is reasonably well understood, there is relatively little information on phytoplankton size classes. The current study shows how phytoplankton of different size classes respond to nutrient enrichment caused by vertical convective mixing during the Northeast Monsoon [(NEM) November-February] and coastal upwelling during the Southwest Monsoon [(SWM) June-September] in the Eastern Arabian Sea (EAS). In the Northeastern Arabian Sea (NEAS), phytoplankton biomass [Chlorophyll-a (Chl-a)] and primary production (PP) were moderate and comparable during both the NEM (Chl-a av. 21 mg m−2 and PP av. 601 mg C m−2 d-1) and the SWM (Chl-a av. 27 mg m−2 and PP av. 516 mg C m−2 d-1). The Southeastern Arabian Sea (SEAS) was oligotrophic (Chl-a av. 12 mg m−2 and PP av. 197 mg C m−2 d-1) during the NEM due to strong surface stratification, but due to coastal upwelling, it turned into a very productive system along the shelf waters during the SWM (Chl-a av. 45 mg m−2 and PP av. 1201 mg C m−2 d-1). Interestingly, the subsurface Chl-a maximum (SCM) was almost absent in the NEAS during both seasons. Similarly, SCM was absent in the entire coastal upwelling zone of the EAS during the SWM. In these areas and situations, Chl-a was found to accumulate in the nutrient-rich surface layers of the shallow euphotic zones. The nutrient enrichment of the coastal upwelling along the shelf waters in the EAS favoured the growth of larger micro-and meso-phytoplankton during the SWM [av. 43.8 mg m−2 (av. 65.9% total Chl-a)], whereas the entire NEAS favoured the growth of nano-phytoplankton during the NEM [av. 13.9 mg m−2 (av. 64.8% total Chl-a)]. Differences in the physical processes enabling the entrainment of nutrients (Nitrate (NO3), Phosphate (PO4) and Silicate (SiO4)] into the euphotic layer could explain the observed differences in the phytoplankton size fractions. The convective mixing in the NEAS during the NEM erodes the bottom of the mixed layer (50–120 m), resulting in only moderate enrichment of NO3 (av. 0.62 ± 0.45 µM) and SiO4 (av. 3.01 ± 0.83 µM), and low level of PO4 (av. 0.49 ± 0.13 µM) in the mixed layer (av. 60 m). This caused N -limitation in the NEAS, which favoured the dominance of nano-phytoplankton. Alternatively, coastal upwelling during the SWM drives deeper subsurface waters (75–150 m) into the shallow surface mixed layer (av. 30 m) in shelf water, causing significant enrichment of NO3 (av. 11.02 ± 3.55 µM), SiO4 (av. 18.34 ± 11.37 µM) and PO4 (av. 1.15 ± 0.21 µM). The enhanced nutrients in the coastal upwelling zones favoured the dominance of larger micro and meso-phytoplankton. However, during the SWM, the oceanic waters of the entire EAS showed low nutrient concentration compared to the shelf waters, which favoured the dominance of nanophytoplankton. In conclusion, our work reveals the large contribution of nano-phytoplankton in Chl-a biomass across the entire EAS, underlining their ecological relevance in both N-limited and N-enriched environments.