Increased nutrient and sediment loading can affect the functioning and biodiversity of coastal ecosystems. Lacking long-term monitoring data, paleolimnological techniques enable the estimation of habitat and diversity change through time. Using these methods we assessed the effects of eutrophication on diatom community structure and species richness over the past ca. 200 years in coastal waters of the Gulf of Finland. The abundance of planktonic diatoms has increased markedly because of increased eutrophication and turbidity. The loss of benthic habitats resulted in a clear decrease in diatom species richness after a threshold of 400-600 microg L(-1) total dissolved nitrogen; no unimodal pattern between diversity and productivity was observed in our data. The urban sites displayed a marked decrease in species richness starting in the late 19th century with increased urbanization. A clear recovery was visible after the cessation of point source loading by the mid-1980s at two sites, whereas at the third site no recovery was detected because of diffuse loading from the large catchment. Changes in the rural sites were minor and did not start until the 1940s.