The western Indian continental shelf is characterized by contrasting biogeochemical features from south to north mostly governed by monsoon wind forcing. Here we present the first detailed study on the phytoplankton community (analyzed by marker pigments and microscopy) during the summer monsoon addressing the interannual variability (Aug 2017 and 2018) along the Western Indian Continental Shelf waters (8° N-21° N, at 200 m isobaths). A distinct interannual variability in monsoon impacted the hydrography and nutrient stoichiometry that was further cascaded to the phytoplankton community structure. The timing of the monsoon onset, wind speeds, and the strength of the alongshore wind component were the major factors that governed the interannual variability in the development and progression of the upwelling as well as phytoplankton bloom. The upwelling-dominated southwestern shelf was characterized by cold, nutrient-rich waters dominated by the marker pigment of diatoms, fucoxanthin, and microscopy also revealed the presence of large, chain-forming diatoms (Chaetoceros sp.; Dactyliosolen fragilissimus). In contrast, low nutrient warm waters in the northern shelf housed nanophytoplankton and picophytoplankton along with small diatoms (Thalassiosira sp.) and dinoflagellates (Gymnodinium sp.). Interestingly, in a few stations in the southern shelf, the surface waters were low saline that was intensified in 2018 compared to 2017 inhibiting upwelled water from reaching the surface. Consequently, due to low nutrient levels caused by reduced upwelling and low salinity, picoplanktonic cyanobacteria dominated replacing the larger diatoms that were found plenty in 2017. Likely, such a niche shift adversely impacted the planktivorous fish catch (Indian Oil Sardine) that was seen to be less in 2018 relative to 2017. Any further changes in monsoon variability and freshwater flow to this region may have direct consequences on the phytoplankton community as well as fisheries.