There is public concern that large-scale disturbances to forest cover caused by insects and storm winds in the Bohemian Forest could intensify high water flows and enhance the expected flooding risks predicted in current regional climate change scenarios. We analysed stream discharge in Upper Vydra and Große Ohe, neighbouring catchments in the Bohemian Forest, the largest contiguous forested area in Central Europe. Upper Vydra, in the Šumava National Park, and Große Ohe (including the Upper Große Ohe headwater catchment in the Bavarian Forest National Park) are similar in size, but differ in land use cover and the extent of disturbed Norway spruce stands. Publicly available runoff and meteorological data (1978-2011) were examined using non-parametric trend and breakpoint analysis. Together with mapped vegetation cover changes, the results were used to address the following questions: 1) are there significant changes in the hydrological cycle and, if so, do these changes relate to 2) the extent and expansion of disturbance in forests stands and/or 3) altered precipitation dynamics and thermal conditions? We found no marked overall change in annual runoff or in annual or seasonal precipitation, but a significant increase in high flows in March. This overall trend related to the marked warming in late winter and early spring (+~4 K in April, p < 0.01), irrespective of altitude and slope position. It significantly shifted the end of the snow cover period by more than three weeks to the beginning/middle of April depending on altitude, and intensified snow melt. In the Upper Große Ohe catchment, a significant decrease in catchment balance, the difference between the long term precipitation and runoff (-72 mm, 11%) was found when the loss of tree cover reached 30% of catchment area. Diminished evapotranspiration losses from severely disturbed stands increased groundwater recharge during summer and caused a significant rise in low flows in autumn. However, observed increases in late winter high flows were due to warming only. They could be further intensified by the increasing winter precipitation predicted under present climate change scenarios, and would therefore increase the risk of flooding at lower elevations.