The temporal and diel changes of cyanobacterial cell density, species composition, and cyanobacterial toxins (microcystin-RR, -YR, -LR) were examined for the outflow water of Lake Suwa in Japan from May to October, 1998. The highest total cell densities of Microcystis were observed in July and September, when the dominant phytoplankton was Microcystis ichthyoblabe and M. viridis, respectively. Both the species composition and total cell density of Microcystis affected the variation of the concentration of three microcystin variants. Only microcystin-RR(MC-RR) and -LR (MC-LR) were detected in July when Microcystis ichthyoblabe dominated, while microcystin-RR, -YR (MC-YR) and -LR were detected in August and October when Microcystis viridis dominated. The microcystin concentration and the cell density of Microcystis in the outflow water showed diel variations; the ratio of maximum to minimum value was $3{sim}20$ fold far microcystin concentration, and $5{sim}31$ fold for cell density. The diel variations of toxin concentration as well as Microcystis cell density was closely related to the diel variation of wind. During the windy period, when higher speeds occurred in the afternoon hours than morning hours, both the cell density of Microcystis and microcystin concentration tended to increase in the morning and decrease in the afternoon. The results of this study suggest that controlling the timing of lake discharge at the floodgate or intake tower can be useful for water resource management with respect to decreasing cyanobacteria biomass within intake water.