|The growing awareness of global warming promotes great interest in investigating the magnitude, spatial, and temporal patterns of the major greenhouse gas (CO2, CH4, and N2O) emissions in the earth systems. The Greenhous Gas (GHG) emissions from inland waters, including rivers, lakes, and reservoirs, remain largely uncertain at the global and continental scales. Empirical-based approaches are widely used to assess the inland water CO2, CH4, and N2O emissions. However, the accuracy of the empirical approaches would substantially decrease with the environmental condition changes mainly due to the inherent weakness in explaining the mechanisms of carbon and nitrogen dynamics in the terrestrial and aquatic systems. Inspired by the improved understanding of the mechanisms controlling carbon and nitrogen dynamics at the terrestrial-aquatic interface, a newly developed scale adaptive water transport model was coupled with the Dynamic Land Ecosystem Model (DLEM) to construct a submodule called – DLEM Terrestrial Aquatic Interface Model (DLEM-TAIM) to better represent the river routing and associated physical and biogeochemical processes. To the best of our knowledge, the DLEM-TAIM is the first process-based model that is capable of concurrently estimating CO2, CH4, and N2O emissions from inland waters. First, we used Chesapeake Bay watershed as a testbed for testing the performance of the coupled model in simulating hydrological processes, river temperature and carbon dynamics at the land-aquatic continuum. Then we nested the inland water GHG model into the DLEM-TAIM modeling framework and applied the coupled model to the Conterminous United States (CONUS). Driven by a gridded dataset at a spatial resolution of 5 arc-minutes, we examined how multiple changes in climate, land use/land cover, elevated CO2, nitrogen deposition and nitrogen fertilizer use affected the GHG emissions from inland water and the relative role of high-order streams and headwater streams in the continental carbon budget for the time period from 1860 to 2018. Our simulation results show that the emissions of CO2, CH4, and N2O from inland waters in the recent decade (2009-2018) were 201.73 ± 30.0 Tg C/year, 7.8 ± 0.6 Tg CH4-C/year , 60.53 ± 8.7 Gg N2O-N/year, which increased by 29.7%, 33.26%, and 58.2% since the 1900s, respectively. The Global Warming Potential (GWP) at the 100-year time horizon (GWP-100 years) for CO2, CH4, N2O from inland waters are 0.73 ± 0.11, 0.04 ± 0.01, 0.29 ± 0.02 Pg CO2 equiv. yr−1, respectively. The total of GWP of the three GHG emissions from inland waters over the CONUS was 1.06 ± 0.13 Pg CO2 equiv. yr−1, which is comparable to terrestrial carbon sink over CONUS. Thus, the continental carbon and GHG budget need to consider emissions from inland waters.