The present invention describes a method for controlling growth of harmful algal blooms generated by the red tide organism, Karenia brevis, and other harmful algal species. The method includes the steps of applying seawater containing low levels of dissolved ozone directly onto or under the surface of water containing harmful algal blooms. Since only low levels of ozone are required for this method to be effective and since the application of ozonated seawater is directed to the bloom itself, release of excess ozone into the atmosphere and/or surrounding water is minimal, which is advantageous since it greatly reduces adverse effects of ozone on the environment, marine life, and human health. The low concentration of ozone utilized in this method is sufficient to destroy the red tide organism, but leave surrounding marine life unharmed.