An increase in severe precipitation events of higher intensity are expected to occur in the southeastern Mediterranean due to intensification of the hydrological cycle caused by climate change. Results of the climate change model’s precipitation data for the period 1970–2100 show a decreasing trend of daily precipitation but of higher intensity. Post-flood field investigation from a severe rainfall event in a small ungauged basin located in northwest Crete produced a validated flow hydrograph, and in combination with two high-resolution digital elevation models (DEMs), were used in the 1D/2D HEC-RAS (Hydrologic Engineering Center’s River Analysis System model), in order to determine the flooded area extent. Lateral structures were designed along the stream’s overbanks, hydraulically connecting the 1D streamflow with the 2D flow areas behind levees. Manning’s roughness coefficient and the weir coefficient were the most crucial parameters in the estimation of floodplain extent. The combined 1D/2D hydraulic model provides more detailed results than the 1D model with regards to the floodplain extent at the peak outflow, maximum flood depths, and wave velocities. Furthermore, modeling with a DEM at 2 m spatial resolution showed more precise water depth output and inundated floodplains. Scenarios of increasing peak precipitation for the same event precipitation depth were used to identify the flood extent due to an increase in daily rainfall recorded by adjacent meteorological stations. These simulation results can be useful in flood risk mapping and informing civil protective measures in flood basin management, for an effective adaptation to increased flood risk caused by a changing climate.