After 60 years of receiving treated sewage effluent from the city of Lahti, Lake Vesijärvi had become very eutrophic. Diversion of the effluent in 1976 resulted in a slow recovery of the water quality. In 1989–93, biomanipulation removed 380 kg of coarse fish per hectare from Enonselkä, the most polluted basin of the lake. Since then cyanobacterial blooms have decreased and water transparency has increased. Paleolimnological analysis of deep water sediments was used to reconstruct the changes in the diatom community, with varved sediment structure providing a year-by-year chronology. During the biomanipulation period the following diatom species increased in Enonselkä: Asterionella formosa, Fragilaria crotonensis, Stephanodiscus heterostylus and Tabellaria spp. In contrast, diatom species commonly considered to be indicators of eutrophication, such as Aulacoseira islandica, Diatoma elongatum and Stephanodiscus parvus, have decreased since the end of the 1980s reflecting the recovery of the Enonselkä basin. The changes in the diatom plankton recorded in the less polluted basin of Laitialanselkä were much less marked than those recorded from the sediments of the Enonselkä basin. In 1990 a diatom species, Actinocyclus normanii f. subsalsa, appeared for the first time in Lake Vesijärvi and since then it has been one of the dominant diatoms in the plankton of the Enonselkä basin. Two years later it was also present in small numbers in the plankton of Laitialanselkä, the least polluted basin of the lake. The appearance of A. normanii f. subsalsa was concomitant with the dredging of the boat harbour of Lahti city in the late summer of 1990. It was therefore apparently not directly affected by biomanipulation but benefited indirectly from the collapse of cyanobacterial populations that led to improved light and nutrient availability in the water column.