Ultrasonic treatment, a relatively less explored technology in water disinfection, was used to quantify the energy required for the destruction of larvae of barnacle Balanus amphitrite, which is a major marine fouling and a potential invasive organism. Since the power used and treatment time for disinfection are economically, and practically, the most important parameters, the energy required to pulverize the larvae into pieces ≤30 µm was determined as a function of the acoustic power density. The present investigation suggests that an ultrasonic system operating at 20 kHz and 0.0975 W/cm3 can effectively pulverize barnacle larvae having length (~440 µm) and breadth (~350 µm) within 45 seconds using 0.1 mJ/larva of pulverization energy. It was also observed that following pulverization of the larvae, the bacterial abundance increased and the rate of release of bacteria was dependent on power level and treatment time, which in turn decided the pulverization rate and hence the rate of release of bacteria.