Drainage networks have been recognized as an active component of regional carbon cycles as streams and rivers receive and mineralize a large amount of land-derived organic matter. However, no quantitative study has ever been performed on the respiration of terrestrial organic carbon in lotic ecosystems at the whole basin scale. By using stable isotope models and ecosystem metabolism measurements, we estimated the amount of land-derived carbon respired by lotic food webs across the Fuji River watershed. We found that small streams tended to increase the flux of terrestrial carbon lost to respiration in this river network. Moreover, larger watersheds with more tributaries decomposed terrestrial organic matter more rapidly than did smaller watersheds, indicating that the presence of small tributaries and the connectivity of those streams to one another accelerate the turnover of fluvial terrestrial organic matter. The present results showed that the connectivity of small tributaries to form large channel network structure affect the basin-scale respiration of terrestrial organic carbon. These findings imply that physical modifications of fluvial geomorphology may affect the delivery of terrestrial organic carbon to coastal areas, thus resulting in change of the strength of land-ocean linkages through riverine carbon flux.