The seasonal reversal of ocean circulation associated with seasonal change in the direction of prevailing winds and the occurrence of several anomalous events in the Eastern Equatorial Indian Ocean (EEIO) make this region dynamic and complex in terms of its biogeochemical characteristics. Two multidisciplinary cruises were conducted to measure nutrients and associated physicochemical parameters across the water column (up to 1000 m) of the EEIO during boreal summer and winter monsoons to understand the distribution of nutrients and their spatio-temporal variability from a biogeochemical perspective. The seasonality in the thermohaline structure of the region is indistinct except for surface salinity drop during summer monsoon due to more precipitation on-site and in adjoining areas. Low concentrations of chlorophyll at the surface and in the deep chlorophyll maxima represent the oligotrophic nature of this region. Surface water was found nutrient-depleted (0.03–0.4 µM Nitrate, 0.02–0.13 µM Phosphate). The maxima of vertical profiles of nitrate and phosphate were recorded at a shallower depth (150–200 m) when compared to its maxima in usual oceanic conditions, but a silicate maximum was recorded in deeper water. In the surface and upper mixed layer paucity of nutrients resulted in low N:P and N:Si ratios. Therefore, nitrogen limitation is evident. The overall ratio of N:P yielded a mean value of 15.33 and matched with the representative literature value for the Indian Ocean. The minimum oxygen values (<50 µM) in the deep water (150–200 m) indicated a hypoxic condition. No signature of denitrification and a moderate nitrate deficit were observed in deep waters. The negative values of Nitrate anomaly (N-tracer) at 50–100 m depth were attributed to a Watermass influenced by denitrification. The prevailing oligotrophic condition caused limited synthesis of organic matter and subsequently little decomposition in deep water. The maxima in the apparent oxygen utilization (AOU) profile are confined to 150 to 200 m depth and represent the most active zone for regeneration that is limited to shallow depth. Regenerated nutrients reached maxima at shallower depth and primarily control material cycling in this region. Supply of nitrate to the surface water based on the preformed values of prevailing water mass was primarily by Bay of Bengal water. According to the findings of this study, preformed nitrate concentrations between 100 and 200 metres below the surface were found very low, indicating that Indonesian Through Flow (ITF) has little impact on the distribution of nutrients in this area.