Floods represent a common process in Tatra Mountain streams and may cause flood risk in the valleys of the Tatra foreland. Dealing with the hazards and risks caused by floods requires a detailed analysis of the frequency and magnitude of past and recent events. However, the Polish Tatra region is characterized by a scarcity of data on past floods in general and on systematic peak discharge in particular. In this study, we performed a paleohydrological analyses in four high-gradient mountain streams using scarred trees as paleostage indicators. We couple two-dimensional hydraulic modelling in a highly-resolved topographic environment (LiDAR data) with an important spatiotemporal data set of scars on trees to investigate (i) the magnitude of unrecorded major floods of the twentieth century, (ii) the effect of variability in geomorphic tree positions on the peak discharge reconstruction, and (iii) the impact of reconstructed events on the results of flood frequency analyses. The data set is based on a total of 55 scarred trees and allows peak discharge reconstruction of 16 major floods covering the last 113 years. Results suggest that trees growing in straight stream reaches or in the inner side of channel bends would be better candidates for peak discharge reconstructions than trees located on the outer side of channel bends or growing in overbank sections with dense vegetation cover. The largest reconstructed flood is dated to 1903 with an estimated peak discharge of 115.9 ± 59.2 m3 s− 1, and larger-than-today floods are found to have occurred at Strążyska and Łysa Polana in the first half of the twentieth century. The inclusion of our results into the flood frequency analyses suggests that flood hazards might have been underestimated by up to 25.5% in the case of a 100-year flood in Strążyski Stream. In that sense, our findings will be useful for the design of future strategies dealing with flood risks in the foreland of the Polish Tatra Mountains.