In glacial lakes on an alpine pasture in Switzerland, benthic cyanobacteria produced microcystin, a cyclic hepatotoxic heptapeptide. The cyanobacteria formed dense mats on sediments and submerged stones. The mats consisted mainly of Oscillatoria limosa, Phormidium konstantinosum (= Oscillatoria tenuis) and Tychonema granulatum (= Oscillatoria granulata). In order to characterize the ecological conditions of these cyanobacteria, nutrient concentrations were determined, and an automatic data acquisition station was installed in one of the lakes. It continuously recorded air temperature, global irradiance, precipitation, atmospheric pressure, wind speed and direction; as well as temperature, pH, oxygen content and conductivity of the lake water. The nutrient situation in the lakes was mainly influenced by the erosion of the gneissic catchment by glacial meltwater and by precipitation. In the glacial lakes, the concentrations of calcium, iron, magnesium, sodium and sulphate increased throughout the summer season. Conductivity values of 4-110 μS cm-1 represent generally low nutrient concentrations. Nevertheless, iron concentrations of up to 20 μM occurred. Biomass, expressed as protein concentration, as well as the microcystin content of the cyanobacterial mats varied within one season and between different years (1994 and 1995). In one cyanobacterial mat community, biomass and microcystin concentrations were highest at the same time, in an other one the microcystin content was maximal three weeks after the highest biomass concentration was reached. Our observations suggest that biomass and toxin production in the mats were strongly influenced by mechanical stress, temporary desiccation and high irradiation.