Climate warming is having a dramatic effect on the vegetation distribution and carbon cycling of terrestrial subarctic and arctic ecosystems. Here, we present hydrologic evidence that warming is also affecting the export of dissolved organic carbon and bicarbonate (DOC and HCO3−) at the large basin scale. In the 831,400 km2 Yukon River basin, water discharge (Q) corrected DOC export significantly decreased during the growing season from 1978–80 to 2001–03, indicating a major shift in terrestrial to aquatic C transfer. We conclude that decreased DOC export, relative to total summer through autumn Q, results from increased flow path, residence time, and microbial mineralization of DOC in the soil active layer and groundwater. Counter to current predictions, we argue that continued warming could result in decreased DOC export to the Bering Sea and Arctic Ocean by major subarctic and arctic rivers, due to increased respiration of organic C on land.