A hydraulic structures in flow (intakes, abutments, spurs, guide banks) damage because of scour at foundations at stratified river bed conditions is an important problem. Influence of the stratification of the river bed on scour development at foundations is confirmed by some authors, but literature analysis shows that there are no methods to find values of the scour depth. The aim of the study is to find the influence of the river bed stratification on the depth of scour at hydraulic structures. Scour at abutments, elliptical and strait guide banks at uniform and stratified bed conditions under steady and unsteady clear-water conditions was studied. Tests were made with uniform grains size sands with one or two layers of different mean size diameters. Different sequence of the stratification was used- fine sand of different thickness on the top of the coarse sand, or coarse sand of different thickness on the top of fine sand. Tests were made with the different hydraulic conditions, contracting rate, Froude numbers of approaching flow and local densimetric Froude numbers. Tests were conducted 7 hours and computer modelling was used to calculate equilibrium stage of scour. New method for computing depth of scour hole at elliptical guide banks at stratified bed conditions is presented. This method allows calculate scour depth in layers with different grain sizes of the river bed materials, thickness and their sequence combination. Method is confirmed by tests results. It was found that depth of scour depends on the grain size, sequence and thickness of the river bed layers. The most critical conditions for structures are when fine sand layer is under the coarse sand layer. When the coarse layer is scoured, depth of scour is rapidly developing in the next fine sand layer. In that case the dominant grain size for computing depth of scour at foundations at stratified bed conditions is mean diameter of the second layer or next, where the scour stops. To calculate depth of scour near hydraulic structures in flow using grain size d50 on the top of the river bed and not to take into account stratification of the river bed, can lead to wrong results and considerable damages and losses.