Understanding the anthropogenic and natural factors that affect runoff water quality is essential for proper planning of water protection and forest management, particularly in the changing climate. We measured water quality and runoff from 10 unmanaged and 20 managed forested headwater catchments (7–12,149 ha) located in Finland. We used linear mixed effect models to test whether the differences in total organic carbon (TOC), total nitrogen (TN) and total phosphorus (TP) export and concentrations observed can be explained by catchment characteristics, land use, forest management, soil fertility, tree volume and hydrometeorological variables. Results show that much of variation in TOC, TN and TP concentrations and export was explained by drainage, temperature sum, peatland percentage and the proportion of arable area in the catchment. These models explained 45–63% of variation in concentrations and exports. Mean annual TOC export in unmanaged catchments was 56.4 ± 9.6 kg ha−1 a−1, while in managed it was 79.3 ± 3.3 kg ha−1 a−1. Same values for TN export were 1.43 ± 0.2 kg ha−1 a−1 and 2.31 ± 0.2 kg ha−1 a−1, while TP export was 0.053 ± 0.009 kg ha−1 a−1 and 0.095 ± 0.008 kg ha−1 a−1 for unmanaged and managed, respectively. Corresponding values for concentrations were: TOC 17.7 ± 2.1 mg L−1 and 28.7 ± 1.6 mg L−1, for TN 420 ± 45 µg L−1 and 825 ± 51 µg L−1 and TP 15.3 ± 2.3 µg L−1 and 35.6 ± 3.3 µg L−1. Overall concentrations and exports were significantly higher in managed than in unmanaged catchments. Long term temperature sum had an increasing effect on all concentrations and exports, indicating that climate warming may set new challenges to controlling nutrient loads from catchment areas.