Bacteria play a crucial role in the Arabian Sea ecosystem by actively participating in the decomposition of organic matter, facilitating nutrient remineralisation and thereby enhancing overall productivity. This study aims to resolve the spatial and seasonal variations in prokaryotic abundance (PA) and biomass with respect to the physicochemical parameters during Spring Inter Monsoon (SIM, April-May), Summer monsoon (SM, June-September), and Winter Monsoon (WM, October-February) in the eastern Arabian Sea. Prokaryotic abundance and biomass distribution estimated using microscopic techniques revealed their highest abundance during SIM, ranging from 2.29 to 4.41 × 106 Cells mL-1 and 8.39 to 21.82 µgL-1, respectively. Similarly, high PA and biomass were observed in late SM (September), ranging from 2.01 to 3.96 × 106 Cells mL-1 and 8.74 to 16.70 µgL-1, respectively, which was preceded by a higher abundance of phytoplankton (Chlorophyll a- 14.57 mg m-3) during peak SM (August). Spatially, the mid-photic waters (M, 75–100 m) sustained high PA during winter convective mixing (January-February). DistLM analysis revealed that ammonia, dissolved oxygen and temperature were the most important factors influencing the PA in the upper photic zone. In contrast, nutrients such as silicate, nitrate, nitrite, and phosphate were the major determining factors in the deeper disphotic waters (200–2000 m) which sustained a stable PA throughout the study period. This study throws light on the intricate interplay between physicochemical and biological variables in shaping prokaryotic population during various physical forcings such as upwelling and convective mixing through intense sampling efforts in the Arabian Sea.