The fate of microcystin in the aquatic ecosystem has been investigated by many researchers throughout the world. Possible pathways of microcystins in Lake Suwa were studied from five per-spectives: production, adsorption, physiochemical decomposition, bioaccumulation and biodegradation. Temporal variability in the concentration of microcystin was investigated during the warm seasons of eight years (1991-1998) in the lake. High concentrations of intracellular microcystin were found during the exponential growth phase of the blooms, whereas concentrations of extracellular microcystin were highest at the end of the blooms. However, concentrations of extracellular microcystin remained very low compared to the levels of intracellular microcystin. The relatively high percentages of microcystin in filtered lake water at the end of blooms suggests that the release of microcystin from cells occurs during senescence and the decomposition period of Microcystis cells.<BR>Freshwater unionid bivalves, Anodonta woodiana, Cristaria plicata and Unio douglasiae, bioaccumulated the microcystins into mussels in the lake. Microcystins were detected in the hepatopancreas (53% of total microcystin in the mussel), gill and muscle (34%), gonad (6%) and gut (7%) of U. douglasiae. The maximum concentration of microcystin in the hepatopancreas of bivalves, was 12.6 (A. woodiana), 297 (C. plicata), and 420 (U. douglasiae) μg g^-1 dry weight, respectively. A bacterium, a new species or even a new genus capable of degrading microcystins-RR, -YR and -LR, was isolated from the lake. When the bacterium was added to microcystins present in a culture medium, the microcystins were degraded thoroughly in a few days. The degradation rate was strongly dependent on temperature the maximum rate was at 30°C.<BR>The presence of a cyanobacterial toxin can be a potential threat, and therefore water treatment re-quires more attention. A complete understanding of the mechanism of microcystin degradation in the ecosystems requires more intensive study, including a quantitative enumeration of microcystin-degrading bacteria. This should be done in conjunction with a study on the microbial ecological mechanism of the degradation of cyanobacteria itself.