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To ensure the good chemical status of surface water across Europe, it is necessary to increase research on the comprehensive impact of land use and land cover changes, i.e., deforestation, on the natural environment. For this reason, we used data from 9-year environmental monitoring in the Wüstebach experimental catchment of the TERENO (Terrestrial Environmental Observatories) network to determine the impact of partial deforestation on solute fluxes and stream water ionic composition. In 2013, a partial deforestation experiment was conducted in the study area using a cut-to-length logging method. To this end, two headwater catchments were compared: one partially deforested (22% of the catchment area) and one untreated control catchment. The concentrations of ions in stream water, groundwater, and precipitation were analyzed: Ca2+, Mg2+, Na+, K+, Al3+, Fetot, Mn2+, NO3−, SO4−, and Cl−. Most of the ions (Na+, Ca2+, Mg2+, Cl−, and SO4−) showed decreasing trends in concentrations after deforestation, indicating a dilution effect in stream water due to the reduction of the supply of solutes with precipitation in the open deforested area. The fluxes of these ions decreased by 5–7% in the first year after deforestation, although the stream runoff increased by 5%. In the second year, the decrease in ion fluxes was greater, from 6% to 24%. This finding confirms that only limited soil erosion occurred after the deforestation because the soil was well protected during logging works by covering harvester lanes with branches. Only K+ and NO3− ions showed increasing trends in both concentrations and fluxes in the partially deforested catchment in the first two to three years after deforestation. Spruce die-offs, common in Europe, may decrease the concentration and fluxes of base cations in surface water in a nutrient-limited environment. However, the simultaneous planting of young broad-leaved trees with post-harvesting regrowth could create a nutrient sink that protects the catchment area from nutrient depletion.