Blue-green algae or cyanobacteria comprise a diverse group of organisms, all of which generate potent natural toxins, as well as characteristic odours. In particular, blue-green algae, such as Microcystis and Anabaena, are often detected abundantly in surface water used as a drinking water resource. In order to confirm our ability to provide safe drinking water even during a water bloom, we have conducted an investigation into the vertical distribution of algae during aeration prior to entry into the intake tower at a dam site. Our analysis of the vertical algal distribution during aeration indicated that aeration occurring at the intake tower exerts a significant influence on the safety of the drinking water. It was determined that the discontinuation of aeration and an increase in the depth at which water intake is conducted, constitutes a viable strategy for the maintenance of toxin- and odour-free drinking water, particularly during water bloom events.