In order to control the growth of Microcystis in aquaculture ponds and reduce its adverse effect on water quality and aquaculture, a production-scale experiment of deep well circulation treatment was carried out in an aquaculture pond with water surface area of 63,000 m2 and water depth of 1.6-2.0 m. Compared with the control pond, the experiment pond had better water quality as indicated by 64.2% reduction in chlorophyll a, and 81.1% reduction in algal cells. The chemical oxygen demand, total nitrogen, and total phosphorus concentration were reduced by 55.1%, 57.5%, and 50.8%, respectively. The treatment efficiency is mainly due to the growth control of Microcystis (i.e. cell reduction of 96.4%). The gas vesicles collapsing because of the water pressure was suggested to be the mechanism for Microcystis suppression by the deep well circulation treatment. The Microcystis lost its buoyancy after gas vesicles collapsed and it settled to the bottom of the aquaculture pond. As a result, the algae reproduction was suppressed because algae could only grow in the area with enough sunlight (i.e. water depth less than 1 m).