The present work presents a methodology based on the use of stochastic weather generators (WGs) for the estimation of high-return-period floods under climate change scenarios. Applying the proposed methodology in a case study, Rambla de la Viuda (Spain), satisfactory results were obtained through the regionalization of the bias-corrected EUROCORDEX climate projections and the integration of this information into the parameterization of the WG. The generated synthetic data series fed a fully distributed hydrological model to obtain the future flood quantiles. The results obtained show a clear increase in the precipitation extreme quantiles for the two analyzed projections. Although slightly reducing the annual amount of precipitation, variations between 4.3% for a return period of 5 years in the mid-term projection and 19.7% for a return period of 100 years in the long-term projection have been observed. In terms of temperatures, the results point to clear increases in the maximum and minimum temperatures for both projections (up to 3.6 °C), these increases being greater for the long-term projection, where the heat waves intensify significantly in both magnitude and frequency. Finally, although rivers may present, in general, with lower flows during the year, flood quantiles experience an increase of 53–58% for high return periods, which reach values of up to 145% when we move to smaller catchments. All this combined translates into substantial shifts in the river flow regimes, increasing the frequency and magnitude of extreme flood events.