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The study characterized the temporal and spatial variability in greenhouse gas (GHG) fluxes (CO 2 , CH 4 , and N 2 O) 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, CO 2 , CH 4 , and N 2 O fluxes ranged from 125 to 536 mg m -2  h -1 , 0.32 to 28.4 mg m -2  h -1 , and 0.16 to 3.14 mg m -2  h -1 , respectively. The habitats (M3 and M5) exhibited higher GHG fluxes than the others. The CH 4 flux followed the summer > autumn > spring > winter hierarchy. However, CO 2 and N 2 O fluxes followed the summer > spring > autumn > winter. CO 2 fluxes were primarily governed by ST and SOC. However, CH 4 and N 2 O fluxes were mainly regulated by ST and SMC (v/v) across the habitats. In the case of N 2 O 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., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)