The paper aims to assess the impact of deforestation due to windstorms on runoff in small mountain river basins. In the Boca and Ipoltica River basins, changes in forested areas were assessed from available historical and current digital map data. Significant forest losses occurred between 2004 and 2012. During the whole period of 1990–2018, forested areas in the Boca river decreased from 83% to 47% and in the Ipoltica River basin from 80% to 70%. Changes in runoff conditions were assessed based on an assessment of changes in the measured time series of the hydrometeorological data for the years 1981–2016. An empirical hydrological model was used to determine the design peak discharges before and after significant windstorms were estimated for different rain intensities and return periods. The regional climate scenario for the period 2070–2100 was used to assess the current impact of climate change and river basin deforestation on predicted changes in design floods in the coming decades. The effect of deforestation became evident in the extreme discharges, especially in future decades. In the Boca River basin, the estimated design floods increased by 59%, and in the Ipoltica River basin by 172% in the case of the 100-year return period.