AbstractConcentrations of dissolved organic carbon (DOC) from terrestrial sources have been increasing in freshwaters across large parts of the boreal region. According to results from large‐scale field and detailed laboratory studies, such a DOC increase could potentially stimulate carbon dioxide (CO2) production, subsequently increasing the partial pressure of CO2 (pCO2) in freshwaters. However, the response of pCO2 to the presently observed long‐term increase in DOC in freshwaters is still unknown. Here we tested whether the commonly found spatial DOC‐pCO2 relationship is also valid on a temporal scale. Analyzing time series of water chemical data from 71 lakes, 30 streams, and 4 river mouths distributed across all of Sweden over a 17 year period, we observed significant DOC concentration increases in 39 lakes, 15 streams, and 4 river mouths. Significant pCO2 increases were, however, only observed in six of these 58 waters, indicating that long‐term DOC increases in Swedish waters are disconnected from temporal pCO2 trends. We suggest that the uncoupling of trends in DOC concentration and pCO2 are a result of increased surface water runoff. When surface water runoff increases, there is likely less CO2 relative to DOC imported from soils into waters due to a changed balance between surface and groundwater flow. Additionally, increased surface water runoff causes faster water flushing through the landscape giving less time for in situ CO2 production in freshwaters. We conclude that pCO2 is presently not following DOC concentration trends, which has important implications for modeling future CO2 emissions from boreal waters.