Although somewhat debated, it is generally agreed in Europe that small water bodies comprise lentic ecosystems that are shallow (less than 20 m) and have a surface area of a few hectares (less than 10 ha). In Albania, 84 glacial lakes constitute a substantial portion of the aquatic ecosystems that sustain high levels of biodiversity, metabolic rates, and functionality. This paper discusses the integration of ecological sustainability into ecosystem services (i.e., cultural, regulatory, and sustaining services) and the national ecological networks of protected sites. This integration is particularly important in light of recent advancements regarding European integration. It is also important due to the catchment continuum, which addresses biodiversity values and gradients that, in this work, are considered using rotifer communities and aquatic plant species. The main causes of the stressors on small ecosystems are inappropriate land use, water pollution, altered habitats, non-native species introduction, resource mismanagement in basins, inadequate planning, and a lack of sector integration. The glacial lakes reflect climate change elements through: an increased number of dried glacial lakes, so only 84 remain functioning; the water level is slowly being reduced; the oscillation of the water level is steadily increasing; and the eutrophication process is rapidly advancing.