Because Lake Kasumigaura is a water supply for nearby residents, blooms of Planktothrix spp. have been a concern, and the causes of the blooms have been unclear. The aim of this study was to identify the causes of blooms of Planktothrix spp. in Lake Kasumigaura, Japan, and to compare environmental factors during and after its recent blooms. We correlated the occurrence of blooms with environmental factors, including rainfall and wind speed, and used principal component analysis to identify relationships between environmental factors during bloom and non-bloom periods. Phosphate concentrations, water transparency, and wind speed were significantly lower during the times when Planktothrix spp. were dominant. The right combination of these three factors enabled Planktothrix spp. to bloom, but Bacillariophyceae could proliferate if the water column had been mixed well by strong winds, and under those conditions, it would be difficult for Planktothrix spp. to bloom. Torrential rain did not affect the biovolume of Planktothrix spp. In the absence of controls over natural environmental factors, blooms of Planktothrix spp. may continue to occur when environmental conditions such as nutrient levels, light conditions, and mixing state are favorable.