The 8 km² mountainous Isepnica cachment in Poland is a study-site where the efficiency of small structures to mitigate floods with limited side-impacts on the ecosystem are tested. However, two previously existing 8 and 7 meter-high sediment checkdams are dangerously damaged and should be dismantled. Besides, they prevent migrations and are now inefficient because sediments have totally filled them up. Because of this enormous volume of compacted sediment, destroying the dams in one operation would be unrealistic, costly, and would suddenly release sediment into the stream. We therefore propose a gradual removal, by lowering the overspill by stages. Moreover, the main structure can be kept and adapted afterwards for flood mitigation purposes. Numerical simulation were carried out to forecast sediment removal for different scenarios of overspill lowering. The effect of several floods, from moderate to rare, is tested at each stage. Modelling also established the influence of the overspill level on the intensity of riverbed erosion downstream. The onedimensional sediment transport model RubarBe, developed by Cemagref, was used to estimate the quantity of sediments transported by balancing inputs, outputs and exchanges with the bottom. Particularly in mountain rivers, one flood may significantly change the morphology of the river bed. It implies that the model had to integrate unsteady flow and cross sections changes with time. A gradual decommissioning strategy is subsequently proposed to ensure a safe transition towards a final state improving the stream status. Our recommendations include river corridor restoration measures, and transformation of the structures into dry reservoirs blending with the mountainous landscape.