In recent years due to the intensified climate, the prevalent hydraulic failure due to flooding and scour has become one of the primary causes for bridge collapse and failure. However, the empirical scour consideration in design for bridge piles, disregarding of scour morphology, may result in differences in the structural responses, causing unexpected and premature failure modes in bridge foundations. Therefore, this paper aims to address the effect of scour morphology on bridge performance and identify essential hydrological and scour morphological parameters. Considering factors associated with bridge layout, flow field and sediment, this paper first investigates and pinpoints the driving factors of scour morphology and their thresholds that are prone to the polygenetic soil profiles through dimensional stacking. Furthermore, the structural responses of bridges subjected to both hydraulic loading and scour are analyzed via finite element model which is confined to the hydrodynamic similitude. In particular, the overall lateral displacement of pile group as well as the different stress level among piles are investigated and compared under different flooding scenarios with uniform and various scour morphology. Derived from limit states, the critical scour depth difference between front and rear piles is identified along with the related hydrological parameters. The proposed approach is applied to a representative bridge in a riverine setting. The implication of the conducted analysis on bridge scour adaptation is also discussed.