Karst systems are important for drinking water supply. Future climate projections indicate increasing temperature and a higher frequency of strong weather events. Both will influence the availability and quality of water provided from karst regions. Forest disturbances such as windthrow can disrupt ecosystem cycles and cause pronounced nutrient losses from the ecosystems. In this study, we consider the time period before and after the wind disturbance period (2007/08) to identify impacts on DIN (dissolved inorganic nitrogen) and DOC (dissolved organic carbon) with a process-based flow and solute transport simulation model. When calibrated and validated before the disturbance, the model disregards the forest disturbance and its consequences on DIN and DOC production and leaching. It can therefore be used as a baseline for the undisturbed system and as a tool for the quantification of additional nutrient production. Our results indicate that the forest disturbance by windthrow results in a significant increase of DIN production lasting ∼ 3.7 years and exceeding the pre-disturbance average by 2.7 kg ha−1 a−1 corresponding to an increase of 53 %. There were no significant changes in DOC concentrations. With simulated transit time distributions we show that the impact on DIN travels through the hydrological system within some months. However, a small fraction of the system outflow (< 5 %) exceeds mean transit times of > 1 year.