The material for pigment analysis was collected 1–3 times a year from Lake Peipsi-Pihkva in 1983, 1987, 1988, 1991 and 1992–1995. Concentrations of chlorophyll a, b and c (Chla, Chlb, Chlc), pheopigment (Pheo) and adenosine triphosphate (ATP) were measured biweekly in 1985–1986. The mean of all Chla values was 20.2 mg m−1 (median 13.3 mg m−1) indicating the eutrophic state of the lake. Average Chlb, Chlc, Pheo and carotenoid (Car) contents were 3.7 mg m−3, 4.1 mg m−3, 3.0 mg m−3 and 4.8 mg m−3, respectively. The average Chlb/Chla ratio was 22.9%, Chlc/Chla 23.4%, Pheo/Chla 38%, Car/Chla 37% and ATP/Chla 3%, the medians being 14.3, 13.6, 17.5, 39.4 and 1.9%, respectively. The proportion of Chla in phytoplankton biomass was 0.41%, median 0.32%. There were no significant differences in temperature, oxygen concentration, Chla, and ATP between the surface and bottom water; the lake was polymictic during the vegetation period. The Chla concentration had its first peak in May followed by a decrease in June and July. In late summer Chla increased again achieving its seasonal maximum in late autumn. The ATP concentration was the highest during spring and early summer, decreasing drastically in autumn together with the decline of primary production. ATP/Chla was the highest during the “clear water period” in June and early July, which coincided also with the high proportion of Chla in phytoplankton biomass. The highest Chla occurred in November (average 37.2 mg m−3) when Secchi transparency was the lowest (1.05 m). Concentrations of Chlb, Chlc and carotenoids were the highest in August, that of Pheo in June. Concentrations of Chla and other pigments were the lowest in the northern part of Lake Peipsi (mean 14.7 mg m−3, median 12.5 mg m−3) and the highest in the southern part of Lake Pihkva (mean 47.9 mg m−3, median 16.3 mg m−3). An increase of Chla and decrease of Secchi depth could be noticed in 1983–1988, while in 1988–1994 the tendency was opposite.