The long-term impact of natural and human-induced large-scale changes on aquatic phanerogams and charophytes has remained mostly unstudied in the Baltic Sea, largely because of a lack of historical data. A vegetation data set based on transects in an estuary in the western part of the Gulf of Finland studied in the 1930s–1940s, however, exists. We re-surveyed 91 of these transects in 2005 and 2007. The historical data set included 60 species and the contemporary 52 species. The species were classified into increasing, decreasing or unchanged according to the change in their occurrence frequencies. A significant frequency change was found for 31 of the 50 (62%) species which were present in both surveys. The proportion of species/growth forms with high-nitrogen and low-light preferences increased, whereas that of species/growth forms preferring oligotrophic conditions and species of shallow waters decreased. In the area, the species expanded their distribution ranges mainly towards the open sea. Eutrophication, reduced grazing pressure and shore overgrowth by Phragmites australis are suggested as the main reasons for the observed changes. In addition, increased boating and shore-construction activities contributed to the long-term floristic changes.