Enclosure experiments were performed at Akanoi Bay, Lake Biwa, in 1995 to determine whether the blooms of cyanobacterial algae changed thermal stratification in the lake. We used four rectangular enclosures, each 10 m × 10 m, with a volume of 200 m3, which were open to the sediments. Two enclosures, A and B, were mixed artificially by aquatic pumps from 1000 to 1400 every day, and the other two enclosures, C and D, were controls with no mixing. The experiment was conducted during late summer from August 3 to September 27. Chlorophyll a concentrations were highest in enclosure D, followed by enclosure C, both of which were controls without mixing. Enclosure A had lower concentrations than enclosures C and D, and enclosure B had the lowest concentrations. No large cyanobacterial algae blooms of Anabaena sp. and Microcystis sp. were seen in the mixed enclosures A and B. In enclosures C and D, blooms of Anabaena sp. occurred in the middle of August, and Microcystis sp. later became dominant in enclosure D at the end of August. In enclosure D, the water temperature changed over the diel cycle before August 17, with thermal stratification during the day and complete mixing at night. After August 17, as Anabaena sp. and Microcystis sp. became dominant, the temperature at the bottom of the enclosure did not change clearly over the 24-h cycle. The APE (available potential energy) density (a measure of water column stability) in the enclosures increased by almost 100% when the biovolume of Anabaena sp. + Microcystis sp. exceeded 20 mm3 l−1. These results indicate that blooms of Anabaena sp. and Microcystis sp. can increase the available potential energy in the water column and create more stable stratification for their growth.