Cyanotoxins in aquatic ecosystems have been investigated by many researchers worldwide. Cyanotoxins can be classified according to toxicity as neurotoxins (anatoxin-a, anatoxin-a(s), saxitoxins) or hepatotoxins (microcystins, nodularin, cylindrospermopsin). Microcystins are generally present within cyanobacterial cells and are released by damage to the cell membrane. Cyanotoxins have been reported to cause adverse effects and to accumulate in aquatic organisms in lakes, rivers and oceans. Possible pathways of microcystins in Lake Suwa, Japan, have been investigated from five perspectives: production, adsorption, physiochemical decomposition, bioaccumulation and biodegradation. In this study, temporal variability in microcystins in Lake Suwa were investigated over 25 years (1991~2015). In nature, microcystins are removed by biodegradation of microorganisms and/or feeding of predators. However, during water treatment, the use of copper sulfate to remove algal cells causes extraction of a mess of microcystins. Cyanotoxins are removed by physical, chemical and biological methods, and the reduction of nutrients inflow is a basic method to prevent cyanobacterial bloom formation. However, this method is not effective for eutrophic lakes because nutrients are already present. The presence of a cyanotoxins can be a potential threat and therefore must be considered during water treatment. A complete understanding of the mechanism of cyanotoxins degradation in the ecosystem requires more intensive study, including a quantitative enumeration of cyanotoxin degrading microbes. This should be done in conjunction with an investigation of the microbial ecological mechanism of cyanobacteria degradation.