ABSTRACTA three‐dimensional coupled hydrodynamic and sediment transport model was employed to simulate the suspended sediment transport at a section of the Danube River, in Hungary. The case study is characterised by a highly complex hydromorphological system due to the nearby tributary inflow, the high number of river regulation structures as well as the several side‐arms connected to the Danube mainstem. The numerical model is set up, parameterised and validated against thorough field data of flow velocities and sediment concentrations measured at different hydrological regimes. Through the selected case study, the paper introduces (i) why 3D description is necessary at a reach‐scale analysis of complex hydromorphological systems; (ii) what sort of field data is needed to parameterise and validate a hydrodynamic and sediment transport model considering the spatial inhomogeneity of the flow and sediment features and (iii) an example for a quantitative impact assessment of side‐arm revitalisation measures on the sedimentation processes, playing a crucial role in the quality of riverine habitats.