Carnivores are threatened worldwide through habitat loss and persecution. Habitat destruction is a major threat for the Eurasian otter. Its populations declined drastically in Europe but are now expanding again, including into the Alps. Here, flood prevention and hydropower have massively altered the riverine landscapes. We evaluated the recovery potential of otters by testing the impact of major factors of habitat transformation and human disturbance on multiple spatial scales. In a hierarchical approach, we investigated spatial use and foraging habitat selection of nine otters in a long-term radiotracking study in the eastern Central Alps. We combined fine scale habitat selection analysis with individual movements by applying a step-selection function approach to the linear river system in a novel way. At home range scale, otters preferred the main riverbeds to abstracted water and tributaries, whereas at fine scale, there was no significant preference for pristine sections within the watercourses. Otters selected for reservoirs in streams with a width smaller than 12 m and otherwise preferred foraging in residual waters and stretches with main discharge. At this stage of recovery, otters show a surprising flexibility in their habitat selection. This is promising for the species' future expansion into former abandoned areas. However, given that the traditional fish stocking regime might contribute to this recovery by providing profitable hunting grounds after stocking events, there is an increased risk of human-wildlife conflicts. Our results demonstrate a high adaptability of a threatened carnivore to altered landscapes and show how this flexible behaviour opens opportunities for recovery.