Using toxic dinoflagellates and their resistant resting cysts as model organisms, we demonstrate the potential of heat treatment as a method to minimise the transport of harmful aquatic organisms via ships' ballast water. Vegetative dinoflagellate cultures of Gymnodinium catenatum could be readily killed using temperatures as low as 35 °C and treatment times in the range 30 minutes to 5 h. The resistant resting cysts (hypnozygotes) of G. catenatum were killed after 2 h at 35 °C and the cysts of Alexandrium catenella were killed after 4.5 h at 38 °C. A careful assessment of various waste heat sources on the BHP bulk carrier 'Iron Whyalla' has confirmed the practicability of this approach, and a successful pilot heat treatment plant was trialled on-board ship in April 1997.