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Predicted increases in the human population, in a context of climatic change and limiting freshwater resources, have raised awareness of the need to preserve aquatic ecosystems, their functions, and the biodiversity they harbor. The ecological reconciliation approach proposes the long-term co-existence of biodiversity preservation and the development of human activities. We investigated the ecological and evolutionary contributions of irrigation and hydroelectric canals in the highly fragmented and regulated Durance River (Rhone basin, Southern France), to the genetic diversity patterns of two interbreeding cyprinid species, the native Parachondrostoma toxostoma, and the introduced Chondrostoma nasus species. We observed a high degree of genetic homogeneity along the length of the river. The maintenance of gene flow despite the presence of dams, and the detection of admixed populations and hybridization events in canals suggest that these canals may act as ecological corridors and hybrid zones with the potential to influence genetic resources for the native and introduced species. These anthropogenic structures vary considerably in terms of their spatial organization, size, and overall management, increasing habitat diversity in the urbanized section of river. Together with the restoration of natural habitats, canals can be considered as important structures for biodiversity dynamic in such urban conditions.