Marine macrophytes and ‐algae have undergone major changes in abundance and species composition over the last decades, primarily due to eutrophication. However, comparable studies conducted in the mid 20th century are rare, but potentially valuable for enabling insight into changes in the benthic communities from the early onset of the eutrophication of the Baltic Sea. In the present study, the submerged phytobenthic community in the exposed southern archipelago of the Åland Islands was examined in 2018 and compared with surveys conducted in 1956 and 1993, respectively. The aim was to analyze long‐term changes in the phytobenthic community in relation to the general large‐scale anthropogenic drivers since the 1950s. Between 1956 and 1993, a decrease in the total number of species/taxa, an increase of filamentous algae coverage and a decrease in the depth range of Fucus vesiculosus was observed. These changes in the phytobenthic community continued between 1993 and 2018, suggesting no changes in the previously described negative trends. Between 1956 and 2018, a general shift in the distribution of phytobenthic functional groups, (grouped according to morphology and type of algae; green, brown and red) occurred, with increased coverage of filamentous brown and green algae, and decline in red algae coverage. The depth range of F. vesiculosus also decreased by >50% between 1956 and 2018. The results support findings that the eutrophication of the northern Baltic Sea is still at a high level, which slows down or prevents the recovery of offshore phytobenthic communities, despite the progress seen in other areas. Thus, the likely main drivers behind the changes are the direct and indirect effects of eutrophication in combination with warmer water, i.e. an effect of climate change.