Abstract: We present an overview of long-term changes in the floristic composition and growth areas in L. Peipsi (3555km2, unregulated water level) that have occurred since the 1960s and a list of plant taxa containing 140 species of higher plants and 4 charophytes. A significant correlation was found between the relative abundance and frequency per stations (Fs) (Rs=0.93). Data on five inhabitants of the eulittoral revealed significant (p <0.05) inter-annual differences in Fs. Comparison of the data of Fs for 67 taxa for 1970–1980 (87 stations) and 1997–2007 (139 stations) showed a significant change in the Fs distribution (p <0.03) and a decline (p <0.05) for 20 taxa; for 15 species Fs had decreased two times or more. However, 14 of the markedly declined taxa, e.g. the long-term dominating submergent Potamogeton perfoliatus, belong still among the top 33 in the list. A significant (χ 2 =11.8; p <0.028) change was observed in the species number of different frequency classes. The number of taxa in the Fs class 46–100 (92)% was 17 in 1970–1980 but only 3 in 1997–2007. The top of the list of macrophytes is dominated by circumpolar species and vicariants. Impoverishment of the flora in the course of eutrophication is expressed by the decrease in Fs; at the same time, the total number of species had not changed. Among the 20 declined taxa 14 are characteristic of the temporarily flooded and/or shallow-water zone of eutrophic water bodies (amphibious and emergent plants); the remaining taxa are shallow-water submergents. The simpliest explanation for their decrease is the expansion of thick reeds occupying suitable eulittoral habitats. [Copyright &y& Elsevier]