The introduction of non-indigenous marine species to foreign environments through the medium of ballast water has led to a research focus on the design of onboard ballast water treatment systems. Such systems must be capable of meeting new International Maritime Organization (IMO) standards while also having minimal effect on the environment and on the operational costs and safety of the vessel. Thermal treatment of ballast water appears to be a promising solution, although the application of low-temperature treatment methods may be limited by the time required for the process. A thermodynamic model is presented for a two-stage heat exchanger system to be used for high-temperature treatment of ballast water during discharge. The model may be used for estimation of ballast water treatment requirements during the design phase for a vessel. It was also used to size a pilot-scale, high-temperature treatment system that has been tested onboard ship with regard to the biological effectiveness of the treatment method.