Repeat measurements (nine times) of nutrients at seven to ten coast-offshore transects along the eastern Arabian Sea (EAS) in 2018–19 revealed nitrogen as the major limiting nutrient controlling the primary production. The summer monsoon upwelling at varying extents along the EAS and the winter convection in the north EAS primarily controlled the depth of nitracline (DNO3 = depth of ≥ 3 µM NO3–). DNO3 was found positively aligned with the upper boundary of thermocline (depth of 26 °C isotherm or D26), with the strongest relationship in the south EAS (R2 = 0.96) due to its relatively stratified and stable conditions during most of the year compared to the north EAS (R2 = 0.71) which is unstable during winter convection. Mixed layer nutrient availability varied with DNO3/D26 and relatively faster nitrogen exhaustion than phosphorus during the nutrient enrichment events viz. upwelling and convective mixing yielded low N/P ratios. The N/P ratios of nutricline waters upwelled/entrained to the mixed layers were found significantly low (6–14), especially at the north EAS where perennial denitrifying zone persisted in the intermediate depths. With continued uptake of nutrients by the plankton following the Redfield ratio, the system during oligotrophic inter-monsoons became nitrogen-limited with surplus (excess) phosphate (P*), resulting in the lowest N/P ratios (1.5 ± 0.7) in the mixed layer. This stoichiometrically excess phosphate (P*) in the mixed layer waters was highest during nutrient enrichment events of both the summer and winter monsoons. The reduction in P* along with high cyanobacterial abundance (evident by increased zeaxanthin pigment concentrations) towards the late phase of summer monsoon and fall inter-monsoon indicates the dominance of diazotrophy. This diazotrophy after the nutrient enrichment seasons reduced the P* to almost half (0.22 ± 0.12 µM) which counter balance the N-limiting conditions to some extent in the EAS surface waters. The N-limiting condition can be severe in a global warming scenario, so more observations and extensive experiments are needed to ascertain the capability of diazotrophs to counteract the N-limiting situations by utilising the excess phosphate. The findings of this study are highly beneficial, as such an extensive year-long information on large spatio-temporal variability and their cause factors is available for the first time from the EAS basin, especially to improve the validation and forecasting of biogeochemical models under changing climate conditions. Comparison of present nutrient data with climatology data of World Ocean Atlas showed complete disagreement of silicate, which is an issue of major concern.