AbstractRecent research showed that inland water including rivers, lakes, and groundwater may play some role in carbon cycling, although its contribution has remained uncertain due to limited amount of reliable data available. In this study, the author developed an advanced model coupling eco‐hydrology and biogeochemical cycle (National Integrated Catchment‐based Eco‐hydrology (NICE)‐BGC). This new model incorporates complex coupling of hydrologic‐carbon cycle in terrestrial‐aquatic linkages and interplay between inorganic and organic carbon during the whole process of carbon cycling. The model could simulate both horizontal transports (export from land to inland water 2.01 ± 1.98 Pg C/yr and transported to ocean 1.13 ± 0.50 Pg C/yr) and vertical fluxes (degassing 0.79 ± 0.38 Pg C/yr, and sediment storage 0.20 ± 0.09 Pg C/yr) in major rivers in good agreement with previous researches, which was an improved estimate of carbon flux from previous studies. The model results also showed global net land flux simulated by NICE‐BGC (−1.05 ± 0.62 Pg C/yr) decreased carbon sink a little in comparison with revised Lund‐Potsdam‐Jena Wetland Hydrology and Methane (−1.79 ± 0.64 Pg C/yr) and previous materials (−2.8 to −1.4 Pg C/yr). This is attributable to CO2 evasion and lateral carbon transport explicitly included in the model, and the result suggests that most previous researches have generally overestimated the accumulation of terrestrial carbon and underestimated the potential for lateral transport. The results further implied difference between inverse techniques and budget estimates suggested can be explained to some extent by a net source from inland water. NICE‐BGC would play an important role in reevaluation of greenhouse gas budget of the biosphere, quantification of hot spots, and bridging the gap between top‐down and bottom‐up approaches to global carbon budget.