Alpine and pre-alpine lotic ecosystems are often remote and not affected by humans, which makes them some of the world’s most pristine ecosystems. However, their status is often altered by the presence of reservoirs that are built to fulfill agricultural needs and hydroelectric demands. These reservoirs also disrupt stream continuity and alter the magnitude, timing, and frequency of natural flows. The present work assessed how high-altitude reservoirs affect the riverine ecosystems focusing on the following: (i) the macroinvertebrate communities, (ii) the breakdown of organic matter, and (iii) the thermal regime. Stretches altered by high-altitude reservoirs had the best conditions for most macroinvertebrate families due to a more stable flow conditions. The breakdown rate of coarse particulate organic matter was not affected by high-altitude reservoirs but its availability was higher in altered compared to pristine stretches. The presence of hydroelectric power plants modified the stream thermal regime. Reservoirs mitigate the atmospheric influence on stream water temperature while run of the river plants strengthen it in the diverted stretches. Where both these alterations were present, the thermal regime of the stream was more similar to the natural ones compared to stretches subjected to only one kind of alteration. This research showed how river impoundment alters the structure of macroinvertebrate communities and the function of the downstream lotic ecosystems and can provide the basis to correctly guide management strategies for lotic ecosystems affected by hydrological alterations.