The study aimed to improve flood hazard assessment in the lower reaches of the Shkumbin River using two-dimensional modeling that takes into account hydrologic uncertainty of the flow. The study compared the extent of the hazard map where the maximum flow includes hydrological uncertainty versus that without hydrological uncertainty. The research methodology included statistical analysis of long-term hydrological observations (1949-1991) from the Rrogozhina hydrometeorological station and two-dimensional hydraulic modelling of floods for the lower reaches of the Shkumbin River (Albania), followed by hazard assessment using Australian classification approaches. This uncertainty was taken into account by accepting the upper limit of the confidence interval with 95% certainty when estimating quantiles for different return periods. The results of the study showed that the extent of the hazard map was directly affected by hydrological uncertainty. The flood hazard index assessment showed an expansion of the map for H1, H2, and H5 by 149%, 67%, and 50%, respectively, for a 100-year return period, confirming the high sensitivity of the floodplain system to hydrological uncertainty. The analysis confirmed the high sensitivity of the lower part of the Shkumbin River to intensive flood processes, which was reflected in the expansion of the risk areas. The analysis also confirmed the importance of the condition of the embankments, since it was precisely the damaged areas where their height is not according to the design that became the reason for the expansion of the flood. The results obtained can be used by water management institutions, spatial planning authorities and civil protection services to develop hazard maps, optimise flood management systems and plan sustainable infrastructure in floodplain areas.