1. We studied the role of zooplankton in biomanipulation and the subsequent recovery phase in the Enonselkä basin of Lake Vesijärvi, using subfossil cladocerans in annually laminated sediment. Measures to restore the Enonselkä basin included reduction in external nutrient loading and mass removal of plankti- and benthivorous fish. Water clarity increased and the lake changed from a eutrophic to a mesotrophic state. However, some signs of increased turbidity were observed after 5–10 years of successful recovery.
2. Annual laminae in a freeze core sample were identified and sliced, based on the seasonal succession of diatoms. Cladoceran remains and rotifer eggs were counted, and Daphnia ephippia and Eubosmina and Bosmina ephippia and carapaces were measured. Annual changes in pelagic species composition were studied with principal component analysis. Individual species abundance, size measurements and various cladoceran-based indices or ratios (commonly used to reconstruct changes in trophic state and fish predation) were tested for change between four distinct periods: I (1985–1988) dense fish stocks, poor water quality; II (1989–1992) fish removal; III (1993–1997) low fish density, improved water quality; IV (1998–2002) slightly increased fish density and poorer water quality.
3. After the removal of fish, the mean size of Daphnia ephippia and Eubosmina crassicornis ephippia and carapaces increased significantly. In contrast, the percentage of Daphnia did not increase. When based on ephippia, the ratio Daphnia/(Daphnia + E. crassicornis) increased, but the interpretation was obscured by the tolerance of fish predation by small Daphnia and by the fact that bosminids were the preferred food of roach. Moreover, ephippial production by E. crassicornis decreased in recent years.
4. The abundance of Diaphanosoma brachyurum and Limnosida frontosa increased significantly after the fish population was reduced, while that of Ceriodaphnia and rotifers decreased.
5. The expanding littoral vegetation along with improved water clarity was clearly reflected in the concentration of littoral species in the deep sediment core. The species diversity index for the entire subfossil community also increased.
6. The period of faltering recovery was characterised by greater interannual variability and an increased percentage of rotifers. Nevertheless, the mean sizes of Daphnia ephippia and E. crassicornis ephippia and carapaces indicated a low density of fish. The deteriorating water quality was apparently related to multiple stressors in the catchment after rehabilitation, such as intensified lakeshore building, as well as to exceptional weather conditions, challenging the management methods in use.