The study characterized the temporal and spatial variability in greenhouse gas (GHG) fluxes (CO2, CH4, and N2O) between December 2020 and November 2021 and their regulating drivers in the subtropical wetland of the Indian Himalayan foothill. Five distinct habitats (M1-sloppy surface at swamp forest, M2-plain surface at swamp forest, M3-swamp surface with small grasses, M4-marshy land with dense macrophytes, and M5-marshy land with sparse macrophytes) were studied. We conducted in situ measurements of GHG fluxes, microclimate (AT, ST, and SMC(v/v)), and soil properties (pH, EC, N, P, K, and SOC) in triplicates in all the habitat types. Across the habitats, CO2, CH4, and N2O fluxes ranged from 125 to 536mgm-2h-1, 0.32 to 28.4mgm-2h-1, and 0.16 to 3.14mgm-2h-1, respectively. The habitats (M3 and M5) exhibited higher GHG fluxes than the others. The CH4 flux followed the summer > autumn > spring > winter hierarchy. However, CO2 and N2O fluxes followed the summer > spring > autumn > winter. CO2 fluxes were primarily governed by ST and SOC. However, CH4 and N2O fluxes were mainly regulated by ST and SMC(v/v) across the habitats. In the case of N2O fluxes, soil P and EC also played a crucial role across the habitats. AT was a universal driver controlling all GHG fluxes across the habitats. The results emphasize that long-term GHG flux monitoring in sub-tropical Himalayan Wetlands has become imperative to accurately predict the near-future GHG fluxes and their changing nature with the ongoing climate change.