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A simple biogeochemical model coupled to an offline ocean tracer transport model driven by reanalysis ocean data is used to simulate the seasonal and interannual CO $_2$ flux variability in the northern Indian Ocean. The maximum of seasonal and interannual CO $_2$ emission variances in the northern Indian Ocean are located in the coastal Arabian Sea (AS) and Southern Peninsular India (SP) with a basin-wide seasonal amplitude and standard deviation of 0.044 $\pm $0.04 Pg C year $^{-1}$. The area integrated CO $_2$ emissions from these two regions in the model are significantly correlated (above a 95 % level) with the observations of Takahashi et al. (Deep-Sea Res-II, 56:554-577, ). The interannual anomalies of CO $_2$ emission from the AS and SP are found as 40 and 30 % of their respective seasonal amplitudes. Both the Arabian Sea (AS) and Southern Peninsular India (SP) interannual CO $_2$ emission anomalies show a 3-4-year variability. The correlations of AS and SP CO $_2$ emission anomalies with the Indian Ocean Dipole/Zonal Mode (IODZM) and Southern Oscillation (SO) indices from 1980 to 1999 are 0.35, 0.21 and 0.32, 0.01 respectively. A 5-year window moving correlation analysis shows that the relationship of AS and SP CO $_2$ emission to the SO and IODZM are complementary to each other. During the years when the correlation of air-sea CO $_2$ emission with the IODZM is stronger, the corresponding correlation with the SO is weaker or opposite. The total change in pCO $_2$ is broken down into changes induced by the individual components such as dissolved inorganic carbon (DIC), sea surface temperature (SST), alkalinity, and salinity and found that (1) the effect of SST in the AS CO $_2$ emission increases (decreases) when the correlation of CO $_2$ emission with the IODZM is positive (negative), and (2) the SP CO $_2$ emission is strongly controlled by the circulation-driven DIC changes; however, this relation is found to be weaker when the SO correlates negatively with the SP CO $_2$ emission. [ABSTRACT FROM AUTHOR]