Sub-tropic Himalayan wetlands play a critical role in regional greenhouse gas (GHG) fluxes and budgets, consequently influencing climate change. Nevertheless, the magnitude, trends, and drivers regulating GHGs fluxes in the sub-tropic wetlands of the Indian Himalayan foothill remain uncertain. Herein, we characterized temporal and spatial GHGs fluxes (CO2, CH4, and N2O) between December 2020 and November 2021 to identify patterns and regulating drivers in the subtropical wetland of the Indian Himalayan foothill. The wetland was divided into five 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) for in-situ measurement of GHGs fluxes (CO2, CH4, and N2O), microclimate (air and soil temperature, soil moisture), soil properties (pH, EC, N, P, K, and SOC). Across the habitats, CO2, CH4, and N2O fluxes ranged between 125.15 to 536.00 mg m− 2 h− 1, 0.32 to 28.35 mg m− 2 h− 1 and 0.16 to 3.14 mg m− 2 h− 1, respectively. The habitats (M3 and M5) exhibited higher GHGs fluxes (CO2, CH4, and N2O) than counterpart habitats. The highest CO2 fluxes were reported in summer, followed by Spring, Autumn, and Winter. However, higher CH4 and N2O flux in summer, followed by Autumn, Spring, and Winter. The soil temperature and SOC were reported as crucial drivers regulating CO2 fluxes than soil moisture. However, soil temperature and moisture equally regulated CH4 and N2O fluxes across the habitats. N2O fluxes were regulated by soil phosphorus and EC across the habitats. The air temperature was a universal driver controlling all GHGs fluxes across the habitats. We urged that long-term GHG fluxes monitoring and identifying drivers across spatiotemporal scales are required to accurately predict GHGs fluxes and budget to understand the warming potential of GHGs in Indian Himalayan wetlands.