The bed changes in a section of the river Danube were computed using a 3-D computational fluid dynamics model. A time series of discharges during the flood in 2002 was used. The results compared reasonably well with regular bed level surveys before and after the flood. The Danube River section was 6 km long and located between Vienna and the Austrian-Slovakian border. The fully three-dimensional numerical model solved the Navier-Stokes equations using the k-epsilon turbulence closure. Nonuniform sediment transport was computed using the formulas of Wu et al. (2000b), considering hiding-exposure algorithms. Both bed deformation and sorting processes were calculated. A number of parameter sensitivity tests were carried out on roughness values, parameters in the sediment transport capacity formula, parameters in the hiding-exposure formulas, critical Shields number, and variations in the formulas for the effect of a sloping bed. Additionally, the sediment inflow to the section was varied together with investigations of physical parameters such as vegetation and groyne structures. The results were most sensitive to the Shields number for critical movement of the sediments. An error analysis was performed to give a quantitative assessment of the parameter sensitivity tests.