The alteration of flow regimes is the most serious threat to the environment and populations of riverine ecosystems. The aim of this study was to verify how newly recovered assemblages of riverine birds react to recent and intensive water control transformations. Data on habitat transformations, breeding bird species and population abundance within submontane river channels in southern Poland were compared before and after river regulation. Regulation works affected approximately one-third of river sections in the drainages studied. Simultaneously, large amounts of gravel, clay and woody debris were removed from river channels, and river channels became overgrown by dense vegetation. Regulation works carried out in river channels, previously restored by severe flood, led to a strong decline in breeding bird assemblages (23% decrease of species richness and 33% decrease of population abundance). These results show that river regulation can significantly alter the structure of breeding bird assemblages, and such change is generally negative for bird diversity (especially for rare and vulnerable species). Riverine habitats are some of the most important biodiversity hotspots and major routes of migration for organisms in Europe, so the degradation of riverine ecosystems can have a catastrophic impact on nature in the entire European Union.