Ditch cleaning (DC) is a forestry practice commonly conducted in boreal regions that aim to lower groundwater tables (GWT) in waterlogged soils, thereby maintaining or improving forest growth. However, there is limited information on the impact of DC on water chemistry and dissolved greenhouse gases (GHG) in draining ditch networks. Based on a repeated synoptic sampling of a paired catchment design we here evaluated water chemistry and GHG data in ditch waters from 25 cleaned sites (being cleaned 1–4 years prior to sampling) and 25 non-cleaned reference sites (REF). The sampled sites were further selected to test whether there were any differences in the DC effect if the operations were conducted in forested or clear-cut areas. Across all sites, we found that DC sites exhibited higher pH, sulfate and calcium concentrations than REF sites. Also, lower dissolved carbon dioxide and higher nitrous oxide concentrations were observed in DC sites. In forested areas, DC sites exhibited significantly higher calcium and potassium concentrations, along with reduced levels of methylmercury and carbon dioxide. In clear-cuts, sulfate concentrations were significantly elevated in the DC sites. We suggest that the observed differences in water chemistry and GHG´s between DC and REF sites were induced by the DC and largely driven by lower GWT following DC, resulting in deeper groundwater flow paths through more mineral-rich soil layers, and altered redox conditions. Also, the removal of organic rich sediments and vegetation from the ditches themselves may affect water chemistry and GHG´s e.g. by decreasing the formation of methylmercury and carbon dioxide.