Ballast water is treated by applying ultrasonic frequencies to the water to kill organisms entrained in the water such as diatoms, veligers, fish larvae, plankton, and microorganisms, preventing the introduction of non-indigenous species between ports-of-call. The ballast water is circulated through a ballast treatment system. A pump is connected to a tube lined with a piezoelectric material for aiding in transmitting the ultrasonic frequencies connected to one or more ballast tanks of a ship. The use of the piezoelectric material as a lining allows a broad range of sound wavelengths and energy levels to be transmitted greater distances before problems with uniform sound penetration and energy loss within the sound field occur. Additionally, spatially-controllable, continuous constructive interference zones may be generated within the piezoelectric-lined tubes to specifically target the particular organisms entrained within the ballast water being treated. The treatment system includes a transducer pipe connected to diffusers and shrouds. The diffusers are closed at ends not connected to the pipe. The treatment system is provided in the ballast intake/drain device to route the ballast water through the treatment system. Ballast water is supplied through inlets in the shrouds into the diffuser which circulate the water through the tube which is lined with piezoelectric transducer material and then exhausted after treatment. The ultrasonic waves destroy organisms and prevent transfer of non-indigenous species between ports.