Arctic ecosystems are very sensitive to the warming climate because of the presence of snow, glacier and frozen soil. As Arctic is warming up, snow and glacier are melting, and frozen soil begins to thaw. The latter may release a large amount of carbon stored in the frozen soil, potentially causing a positive feedback to the global climate system. Dissolved organic carbon (DOC) is the largest reduced carbon and plays an important role in the Arctic carbon cycling. Few studies have quantified how land DOC can be produced and released to aquatic ecosystems. In this study, we developed a three-dimensional ecosystem model to illustrate how DOC can be produced and transferred from land to river. We applied and validated this model to the Tanana Flats in central Alaska. We found that: (1) litterfall plays an important role in releasing DOC during snowmelt and runoff; (2) water flow is key to the redistribution of DOC from land to river; and (3) ten thousand tons of DOC is released into the Tanana River annually from this region. Our study provides a powerful tool to quantify the regional carbon cycling by explicitly considering the carbon export from land to aquatic ecosystems in the Arctic.