Transport system infrastructures, namely roads, bridges, dams, and water intakes in rivers are under permanent impacts of multiple floods. To estimate their safety and stability during scour at hydraulic structure foundations, a multidisciplinary approach, which will involve the principles of hydraulics, hydrology, morphology, geology, and so on, is required. In the present study, the effects of probability, duration, sequence, and frequency of multiple floods on the safety and stability of engineering structures in river flow are studied. In frame of this study the impact of the floods with different shapes of hydrograph on the scour process is investigated.