Logging disrupts the ecology of molecules in headwater streams.

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 where it is more easily rereleased to the atmosphere. Here, we tested how logging changed DOM in headwaters of hardwood-dominated catchments in northern Ontario, Canada. We applied a before-after-control-impact experiment across four catchments for 3 y and measured DOM monthly during ice-free seasons. DOM concentration in streams from logged catchments quadrupled, on average, only for the first 2 mo postharvest, but resulting changes to the molecular composition of DOM persisted for at least 2 y. Ultrahigh-resolution mass spectrometry revealed that DOM composition within logged streams became more available for microbial use 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 postharvest was most similar to the DOM composition of surrounding soils, likely due to increased hydrological connectivity. Alongside carbon being more likely to be released into the atmosphere, we estimate that selective logging increased the total flux of dissolved organic carbon in streams by 6.4% of the carbon extracted as timber. Although these estimates are short-lived, they should affect the millions of hectares that are logged annually. Carbon accounting of forestry, including as a natural climate solution, must now consider the transport and fate of DOM from land into water.