Motivated by the need for additional tools to disinfect discharge water from well boats, and to prevent distribution of salmon lice, the effect of ultrasonic cavitation on the planktonic stages of the salmon louse, nauplii and copepodids, as well as marine heterotrophic bacteria, and the marine green microalgae Tetraselmis suecica, has been investigated. Survival and morphology were registered after different exposure times. Efficacy of the ultrasonic cavitation treatments varied with exposure time. A reduction in survival was registered even for the shortest exposure time (5 seconds) for both naupliar and copepodid stages of the salmon louse (36.7 ± 11.5 and 67.20 ± 7.2% survival respectively). Survival reached zero after exposure times of 20 and 60 seconds for the nauplii and copepodid stages, respectively. A reduction in 70% was observed for bacteria at all exposure times (5 to 300 s), while a reduction of 95% was observed after 300 s for algal cells. The logged energy transfer to the samples was on average 17.5 J/s. In conclusion, cavitation treatment is destructive for the planktonic stages of salmon lice, and may contribute to reduce discharge of pathogens and parasites from well boats when adapted for this purpose and combined with existing water disinfection methods.