Temporal and spatial variation in the concentrations of intra- and extra-cellular microcystins were studied in a hypertrophic lake with bloom of Planktothrix agardhii (Gomont) Anagnostidis et Komarek. Concomitantly with increase in water temperature (from 2 to 20 °C) abundance of P. agardhii increased from 1.9 x 105 to 4.3 x 107 trichomes L-1. In autumn, in spite of temperature lower (14°C) than in summer it was still very high. Mass development of P. agardhii (to 6 x 106 L-1 and higher) caused a severe decrease in water transparency (to 0.5 - 0.2 m in summer/autumn). The cyanobacterium density was relatively uniform within water column; only in summer (July) it was significantly higher (by about 30%) in surface than in bottom layer. From spring to autumn microcystins (MCs) were mainly biomass-bound (up to 90 μg MC-LR equiv. L-1), whereas the level of extra-cellular toxins was much lower (up to 2 μg L-1) and relatively stable. Only in winter, high amounts of MCs (11.3 μg L-1) were released from decaying biomass into water. The increasing concentrations of biomass-bound microcystins in the lake water positively correlated (R2 = 0.9863; y = -0.1285x2 + 7.14x ) with the abundance of P. agardhii and the highest concentrations of the intracellular MC fraction were found during the exponential phase of P. agardhii growth. In addition, the surface-sampled biomass of P. agardhii contained in autumn 2-fold more MCs (2.75 μg MC-LR equiv. per 106 P. agardhii trichomes) than the bottom-sampled one (1.41 μg MC-LR equiv. per 106 trichomes). This is the first report showing that despite the homogenous distribution of P. agardhii in water column of a shallow lake, various seasonal and spatial distributions of both extra-cellular and intracellular fractions of microcystins occur.