Emissions of greenhouse gases (GHGs) from the Indian subcontinent have increased during the last 20 years along with rapid economic growth; however, there remains a paucity of GHG measurements for policy-relevant research. In northern India and Bangladesh, agricultural activities are considered to play an important role in GHG concentrations in the atmosphere. We performed weekly air sampling at Nainital (NTL) in northern India and Comilla (CLA) in Bangladesh from 2006 and 2012, respectively. Air samples were analyzed for dry-air gas mole fractions of CO2, CH4, CO, H2, N2O, and SF6 and carbon and oxygen isotopic ratios of CO2 (δ13C-CO2 and δ18O-CO2). Regional characteristics of these components over the Indo-Gangetic Plain are discussed compared to data from other Indian sites and Mauna Loa, Hawaii (MLO), which is representative of marine background air. We found that the CO2 mole fraction at CLA had two seasonal minima in February–March and September, corresponding to crop cultivation activities that depend on regional climatic conditions. Although NTL had only one clear minimum in September, the carbon isotopic signature suggested that photosynthetic CO2 absorption by crops cultivated in each season contributes differently to lower CO2 mole fractions at both sites. The CH4 mole fraction of NTL and CLA in August–October showed high values (i.e., sometimes over 4000 ppb at CLA), mainly due to the influence of CH4 emissions from the paddy fields. High CH4 mole fractions sustained over months at CLA were a characteristic feature on the Indo-Gangetic Plain, which were affected by both the local emission and air mass transport. The CO mole fractions at NTL were also high and showed peaks in May and October, while CLA had much higher peaks in October–March due to the influence of human activities such as emissions from biomass burning and brick production. The N2O mole fractions at NTL and CLA increased in June–August and November–February, which coincided with the application of nitrogen fertilizer and the burning of biomass such as the harvest residues and dung for domestic cooking. Based on H2 seasonal variation at both sites, it appeared that the emissions in this region were related to biomass burning in addition to production from the reaction of OH and CH4. The SF6 mole fraction was similar to that at MLO, suggesting that there were few anthropogenic SF6 emission sources in the district. The variability of the CO2 growth rate at NTL was different from the variability in the CO2 growth rate at MLO, which is more closely linked to the El Niño–Southern Oscillation (ENSO). In addition, the growth rates of the CH4 and SF6 mole fractions at NTL showed an anticorrelation with those at MLO, indicating that the frequency of southerly air masses strongly influenced these mole fractions. These findings showed that rather large regional climatic conditions considerably controlled interannual variations in GHGs, δ13C-CO2, and δ18O-CO2 through changes in precipitation and air mass.