Cyanobacterial toxins are now reported worldwide from numerous aquatic sites covering both productive and less productive systems. Toxin concentrations may range from < 1 to 8600 μg g dry weight^-1 of algal material often containing more than one type of toxin. A few studies have reported detectable concentrations of dissolved toxins (0.06-1830 μg I^-1) released naturally during the growth cycle of cyanobacteria or in association with the breakdown of cyanobacterial blooms. The toxin concentrations have potentially negative effects on the planktonic and benthic organisms in nature. Species from all trophic levels seem susceptible, although the sensitivity to the toxins varies even within related groups of organisms. Earlier reports on lethal and sublethal effects of toxins include trophic levels from bacteria to fish and some indications of antibiotic and allelopathic effects have also been described. Recent findings suggest that certain phytoplankton and protozoan species are affected by much lower concentrations of toxins than organisms at higher trophic levels. Our knowledge of the ecological consequences of cyanobacterial toxins in aquatic habitats is fragmentary, but possible risks can be identified: diminished growth of microbial organisms, reduced grazing potential of larger zooplankton, failure of sensitive species to develop and establish and accumulation of toxins in the food chains. The food webs are interrupted by the toxins, which may reduce the degradation potential of microorganisms in the pelagic, leaving more material to be decomposed in the sediments. The ecological implications of such events are unclear, but temporal destabilization of natural systems seems possible, which may interfere with lake restoration programmes. Long-term implications are also likely, but this remains speculative.