The species diversity of algae in different ecotopes of the alpine lake Nesamovyte was studied. In total, 233 species were identified comprising globally and regionally rare species. We also documented a temporal change in species composition of algae from the first investigations conducted 100 years ago to present. An increase in the species diversity of Bacillariophyta and Chlorophyta, the constancy of the number of Euglenophyta and Cyanoprocaryota species, a decrease in the composition of Charophyta and the disappearance of Dinophyta species were revealed. We further documented some changes in the most abundant species and indicator species for certain limnological conditions, the disappearance of montane species and the colonization of species with a wide ecological-geographical amplitude. There occurred confinement to benthic and plankton-benthic conditions and the increase of indicators of low-alkaline mesotrophic waters as well as mass development ("blooming") of some species. The studied features of the species diversity of the "algoflora" indicate high species richness and a high number of indicator species, as well as lake ecosystem degradation and an increase in organic pollution. There was a shift of the lake from oligotrophic to mesotrophic state, as indicated by certain algal groups. The noted changes in the species diversity of algae in Nesamovyte Lake could be attributable to the increased anthropogenic influence leading to change of the trophic status of the lake.