Scour development in time at the elliptical guide banks during the floods was studied. The dimensions of the upper part of the elliptical guide banks, namely the turn and length, were calculated by the Latishenko method. The length of the lower part of elliptical guide banks was half of the calculated upper part. The differential equation of the bed sediment movement in clear water is used, and a method for calculating the development of depth, width, and volume of scour hole with time during the floods at the head of the elliptical guide banks is elaborated and confirmed by experimental data. A new method for computing the equilibrium depth, width, and volume of a scour hole at the elliptical guide banks is presented. A comparison of the depth of scour computed after multiple floods with the equilibrium depth of scour allows us to estimate the stability of the elliptical guide banks during the maintenance period.