Future global sustainability depends heavily on the development of renewable energy. The object of this study is a system of two plants (Kaunas hydropower plant (HP) and Kruonis pumped-storage hydropower plant) and upper and lower reservoirs. A possible dam failure accident in such an important system can endanger the population of Kaunas City. The methodology for estimating dam-failure-induced flood wave uncertainty included scenarios of the upper reservoir embankment failure hydrographs, modeling flood wave spreading (MIKE 21 hydrodynamic model), and estimating wave heights. The GRS methodology was selected to assess the uncertainty of flood wave modeling results and the sensitivity of hydrodynamic model parameters. The findings revealed that the discharge values of the Nemunas inflow and outflow through the HP outlets are the most important parameters determining the greatest height of the flood wave. Therefore, by correctly managing the amount of water in the upper reservoir, it would be possible to prevent the lower reservoir dam from breaking.