The present study is undertaken in the eastern coast of India, along the coastal tract of Bay of Bengal (BoB), to delineate the submarine groundwater discharge (SGD)-borne nutrient flux at temporal scale and their impact to coastal ecology and biogeochemical processes. Solutes chemistry, seepage meter study, stable-isotopic signature, and geophysical techniques were used to identify the surface water–groundwater interaction zone, SGD rate and nutrient flux. The estimated rate of major annual discharge of nutrient fluxes were 240 and 224 mM $\rm{m^{-2} day^{-1}}$ for $\rm{NO}_{3}^{-}$ and Fetot. The variation of solute and nutrient fluxes was depending on the load of terrestrial water masses, which is triggered by the local monsoonal meteoric recharge. The ecohydrological response to this solute flux results in spatio-temporal patterns of N and P-sensitive algal blooms in the intertidal zones. Most algae were identified as dinoflagellates and some haptophytes, with greenish and brownish hue that provides a distinct look to the coastal landscape. The algal blooms were found to be substantially influenced by the seasonal-nutrients flux and discharge location. Our study is expected to increase the understanding of a rarely reported ecohydrological response to terrestrial–marine water interactions and their implications in the tropical ocean adjoining the Indian Subcontinent.