In flood modelling, the structure of conceptual models may have a large influence on the simulation results. Hence, the focus of this paper is on the structural uncertainty in hydrodynamic flood modelling systems. Three different conceptual models with an increasing order of complexity of the spatial discretisation of the flow through a polder system were compared in order to investigate the effect of spatial resolution and dimensionality on flood modelling. The hydrodynamic 1D model DYNHYD was used as a basis for the simulations. The model was extended to incorporate a quasi-2D approach and a Monte Carlo analysis was used to show the effect of structural uncertainty on the resulting flow characteristics of the diverted flood waters. Two flood events of the River Elbe were used to calibrate and test the model. The results of the velocity fields indicate that the simplest 1D model revealed more predictive uncertainty than the other two more complex models. The differences in model structure does not cause large differences in the capping of the peak discharges, but may substantially influence the results of subsequent modelling of sediment and contaminant transport.