The intra-seasonal perturbations in the atmospheric weather are closely related to the variability in the ocean circulation. NASA Ocean Biogeochemical Model (NOBM) couples the oceanic general circulation and the radiative forcing. The NOBM model products of nitrate, total chlorophyll, and mixed layer depth (MLD) collected during the period from 1998 to 2007 as well as the sea surface temperature (SST), precipitation, outgoing long wave radiation (OLR), and wind are considered in this study to identify the influence of intra-seasonal oscillation (ISO) of Indian summer monsoon (ISM) on the biogeochemical constituents of Bay of Bengal (BOB) (6°–22° N; 80°–100° E) and Arabian Sea (AS) (3°–17° N; 55°–73.5° E) of North Indian Ocean (NIO). The active and break phases are the most significant components of ISO during ISM. The result of the study reveals that the upper ocean biology and chemistry significantly vary during the said phases of ISM. The nitrate, total chlorophyll, and MLD are observed to be strongly correlated with the ISO of ISM. The result shows that, during ISO of ISM, the concentration of nitrate and chlorophyll is strongly and positively correlated both in BOB and AS. However, the correlation is more in AS, endorsing that the Arabian Sea is more nutrient reach than Bay of Bengal. Nitrate and MLD, on the other hand, are strongly but negatively correlated in the said basins of North Indian Ocean (NIO). The forcing behind the variability of the biogeochemical constituents of BOB and AS during active and break phases of ISM is identified through the analyses of SST, precipitation, OLR, and wind. © 2018, Springer-Verlag GmbH Austria, part of Springer Nature.