Transport system infrastructures are under permanent impacts of multiple floods. To estimate their safety and stability during scour development at hydraulic structure foundations is required. In these studies, the flow parameters at the peak of the flood with unrestricted or restricted duration were used. The effects of probability, duration, sequence, and frequency of multiple floods on the safety and stability of engineering structures in river flow are studied. The impact of the floods with different shapes of hydrograph on the scour process is investigated. The method for estimating the scour development with time was used to perform computer modelling. It was found that the shape of the hydrograph affects the depth, width, and volume of the scour hole developed during the floods. The results obtained in this study and presented in figures and tables confirm our conclusions.