Global changes and local pressures related to the exploitation of water resources are significantly reducing streams' biodiversity and threatening their ecological balance. This trend concerns both the lowland rivers flowing in densely populated areas, and the alpine headwaters, where the effects of global change are dramatically evident and often accompanied by alterations in river hydro-morphology. In mountainous river stretches, regulation and morphological alterations such as bank reinforcement, water abstractions, dams, and weirs are increasing. In the Alps, protected areas and especially large National Parks constitute an effective strategy to face the loss of biodiversity, but little is known about their effectiveness regarding lotic environments. To examine the recent trend in aquatic communities in Alpine protected areas, we carried out biological samplings and hydro-morphological evaluation in twelve high-altitude streams within the oldest Italian National Park, the Gran Paradiso Park, located in the heart of the Western Alps, and we compared results with a previous survey performed in 2005, keeping the same experimental design. Our results detected minimal changes in the hydro-morphology of the studied watercourses. Biomonitoring indices associated with benthic communities likewise do not evidence significant differences. Concerning diatom flora, we found however in 2020 a greater uniformity in species composition compared to communities of 2005, and a slight turnover between species. In conclusion, our findings underline the effectiveness of protected areas for the conservation of running water environments because they limit hydro-morphological alterations thus increasing the resilience of aquatic communities to climate change.