Four gaps of 30 m diameter were cut in a mature European beech (Fagus sylvatica L.) forest in 1989. In two of the gaps and their surrounding areas, dolomite lime (3 t ha−1) was applied. The study was designed to examine the long-term effects of lime application and canopy removal on element input via throughfall and output in seepage water at 80 cm depth in this European beech forest. Throughfall and seepage water were collected in the unlimed gap center, the limed gap center and the undisturbed beech stand in 1991, 1992, 1993, 1996 and 2012. The canopy opening increased the seepage water acidity from 1991 to 1996. The pH values of the seepage water were higher in the limed gaps than in the unlimed gaps during the five study periods. The amount of annual throughfall and of seepage water were higher in the gaps during the study period; in 2012, the annual amounts of seepage water were significantly higher in the gaps than in the closed stand, whereas the input of most elements decreased from 1991 to 2012. The seepage water in the unlimed gaps had higher nitrate nitrogen (NO3-N) concentrations, but lower sulfate sulfur (SO4-S) concentrations than in the limed gaps in 1991, 1992, 1993 and 1996. The amount of leaching NO3-N and SO4-S in 2012 was, however, significantly higher in the limed gaps than in the unlimed gaps, while the input of nitrogen (N) and SO4-S was significantly lower in the limed gaps than in the closed stand. In general, the annual amounts of element input via throughfall were higher in the closed stand than in the gaps. However, the element output through leaching was much higher in the gap centers than in the closed stand. The net losses of aluminum (Al), calcium (Ca), magnesium (Mg) and manganese (Mn) were higher in the unlimed gaps than in the limed gaps and the closed stand in 1991. In 2012, 23 years after liming and canopy opening, the effects of gaps and liming, and the interaction of gap and liming on element leaching, were still significant compared to the untreated stand. Overall, canopy opening reduced N, sulfate, Al, and base cation deposition in the long run. Canopy opening in combination with liming affected the seepage water acidity and the leaching losses of base cations up to 23 years after canopy removal and liming in this European beech forest.