The failure of guide banks because of scour at stratified bed conditions leads to the flow redistribution and an unpredicted scour at the alignment of the bridge crossing; as a result, this can be the reason for failure of piers and/or abutments. In spite of the importance and complexity of the phenomena, the equilibrium stage of scour at the elliptical guide banks under stratified bed has not been studied yet. Based on the condition that at an equilibrium stage of scour is when the local velocity becomes equal to the critical one, formulas for calculating the equilibrium depth of scour at the head of elliptical guide banks at uniform sand and stratified bed is elaborated. The most critical conditions for structures is when fine-sand layer is under coarse-sand layer. When the coarse layer is scoured away, the depth of scour is rapidly developing in the next fine-sand layer. In this case, the dominant grain size for calculating the depth of scour under stratified bed conditions is the mean diameter of the second layer or of the next one, where the scour stops. According to the analysis results the depth of scour is always greater when a fine-sand layer is under coarse-sand layer(s.) The calculation of scour depth near hydraulic structures in flow by using the grain size on the top of the river bed and neglecting the stratification can lead to wrong results and finally to considerable damages and losses. An analysis of the results shows that the equilibrium depth of scour depends on the hydraulic and river bed parameters: contraction rate of the flow, Froude number of the open flow, grain size of the bed material, the stratified bed conditions, the local velocity, shape of the guide banks, the flood probability, water depth on the floodplain, the angle of flow crossing, and the slope of the side wall