Three Scots pine (Pinus sylvestris L.) ecosystems (Rosa, Taura, and Neuglobsow) along a former deposition gradient (sulfur and alkaline dust) in the new federal states of Germany were investigated since 1993. Although deposition rates were drastically decreased after the unification of Germany, element output rates from formerly impacted sites are still high. Both field measurements and laboratory studies show that the organic surface layers release high amounts of sulfur clearly exceeding present input rates. Therefore, accumulated element stores and top soil properties were analyzed. Amounts of water soluble sulfate and dissolved organic sulfur as determined in batch experiments reflect the former deposition gradient and a specific spatial accumulation pattern within the stands. pH, base saturation and C:N ratio in the top soil are clearly influenced by the former pattern of alkaline dust and sulfur deposition. Undisturbed soil columns from the top soils were taken from all sites to investigate element output rates under controlled conditions and at different temperatures. At 5 °C, both calcium and sulfate output decreases in the order Rosa (1.27 mmol m−2 d−1; 0.25 mmol m−2 d−1) > Taura (0.30 mmol m−2 d−1; 0.22 mmol m−2 d−1) > Neuglobsow (0.12 mmol m−2 d−1; 0.12 mmol m−2 d−1). Output rates increase considerably at higher temperature. Mineralization of organic matter seems to be the key process in mobilization of accumulated elements. The rate of mineralization itself and the mechanisms to buffer the acidity produced by both N and S mineralization is affected by the different deposition history of the sites and by the changes in top soil properties induced by the long-term deposition impact. Due to the high element stores accumulated during the period of high deposition rates, the organic surface layer provides a large sulfur pool that will be released mainly by mineralization resulting in long-term sulfate leaching and the risk for future (re)acidification of soils and waters.