The data for the vegetation periods (May–November) of 1997–2005 were used to analyse the dynamics of zooplankton and the most important phytoplankton groups in Lake Peipsi (Estonia). With some fluctuations, a continuous decline appeared in zooplankton abundance and biomass in those years. Since 1997 the share of cyanobacteria in phytoplankton biomass increased continuously: from 20% to 60% in L. Peipsi s.s., and from 30% to 90% in the southern parts of the lake. In 2000, a heavy bloom of Aphanizomenon flos-aquae took place in October–November, and in the following year a significant decrease occurred in zooplankton, particularly in rotifers, and in phytoplankton biomass. In 2002, a very low water level, accompanied by high temperatures in August, caused a strong water bloom and fish kill. In the following years the zooplankton biomass (less than 1 g m–3), particularly that of rotifers, was low. In the southern parts of the lake, the potentially highly toxic cyanobacterium Microcystis viridis started to dominate since August–September 2002. An appreciable concentration of cyanotoxins was detected in both lake parts in the same months in 2002. Possibly, this is one of the reasons for the significant decrease in the biomass of zooplankton, particularly rotifers. Another reason may be the growing grazing pressure of planktivorous fishes and fish fry on zooplankton.
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