Global demand for wood products is increasing forest harvest. One understudied consequence of logging is that it accelerates mobilization of dissolved organic matter (DOM) from soils to aquatic ecosystems. Here, we tested how logging changed DOM in headwaters of hardwood-dominated catchments in northern Ontario, Canada. We apply a before-after control-impact experiment across four catchments for three years. DOM concentration in streams from logged catchments quadrupled, on average, after the first year post-harvest, but resulting changes to the molecular composition of DOM persisted for at least two-years. Ultrahigh-resolution mass spectrometry revealed that DOM within logged catchments was more energy-rich and chemically diverse than in controls, with novel highly unsaturated polyphenols, carboxylic-rich alicyclic, and nitrogen-containing formulae. The molecular composition of stream DOM measured fortnightly post-harvest was most strongly associated with DOM composition within intermediate and deeper layers of contributing soils, likely due to increased hydrological connectivity post-harvest. We estimate logging increased the total annual flux of dissolved organic carbon in streams by 6.4% of extracted wood carbon, and this carbon was more likely to be released into the atmosphere. Carbon accounting of forestry, including as a natural climate solution, must now consider the transport and fate of DOM from land into water.