AbstractInland waters emit significant amounts of carbon dioxide (CO2) to the atmosphere; however, the global magnitude and source distribution of inland water CO2 emissions remain uncertain. These fluxes have previously been “statistically upscaled” by independently estimating dissolved CO2 concentrations and gas exchange velocities to calculate fluxes. This scaling, while robust and defensible, has known limitations in representing carbon source limitations and spatial variability. Here, we develop and calibrate a CO2 transport model for the continental United States, simulating carbon transport and transformation in >22 million hydraulically connected rivers, lakes, and reservoirs. We estimate 25% lower CO2 fluxes compared to upscaling estimates forced by the same observational calibration data. While precise CO2 source distribution estimates are limited by the resolution of model parameterizations, our model suggests that stream corridor CO2 production dominates over groundwater inputs at the continental scale. Our results further suggest that the lack of observational networks for groundwater CO2 and scalable metabolic models of aquatic CO2 production remain the most salient barriers to further coupling of our model with other Earth system components.