Disrupted fluvial dynamics in the Danube downstream of the Gabèíkovo hydropower scheme adversely affected habitat diversity and the hydrological connectivity between the river and its floodplain. The restoration concept developed for one of the most altered reaches of the Slovak-Hungarian segment of the Danube River (rkm 1,810–1,798) focuses on reintroducing of fluvial dynamics and associated lateral connectivity to improve habitat diversity appropriate for rheophilic species and birds. The interaction between ecological restoration of floodplain channels and flood-risk reduction is also addressed. A two-dimensional hydrodynamic model CCHE2D was developed to optimize the flow conditions, the geometry of side channels and the parameters of measures proposed in scenarios applied. Modelling results indicate that the reconnection of floodplain channels and the associated fluvial dynamics may substantially improve the hydromorphological and ecological situation, a step closer to the natural state. The ecological restoration concept is also expected to contribute to flood-risk reduction (~ 22–30 cm for Q₁₀₀) along the Danube River reach.