A method and apparatus are disclosed for treating a liquid with electromagnetic wave energy, particularly in the radio frequency range, wherein the characteristics of the wave energy are selected and controlled to produce optimally beneficial effects with respect to specific substances present in the liquid. The liquid to be treated is analyzed to identify its components, and an energy absorption value for a target component is determined. Electromagnetic wave signals, having characteristics selected to achieve a desired effect on the target component, are generated using a wave signal generator and then directed into the liquid using a wave signal emitter. The wave signal emitter may be in the form of an immersion probe or a transmitting antenna.