Abstract The inhibitory effect of ultrasound on barnacle (Amphibalanus amphitrite) cyprid was investigated under three excitation frequencies (23, 63, and 102 kHz). The linear regression models were built to study the effect of ultrasound pressure and exposure time on the cyprid settlement. The negative slopes of the linear regression lines indicate reduced settlement behavior with increased exposure time and acoustic pressure. The excitation frequency of 23 kHz was found to be the most effective on settlement inhibition, with 63 and 102 kHz exhibiting similar but weaker response. Separately, ultrasonic cavitation was investigated and confirmed in the filtered seawater (FSW) and partially degassed filtered seawater (PDFSW) via the acoustic spectrum analysis. The cavitation energy was found to be double in FSW than in PDFSW at 23 kHz with the acoustic pressure of 20 kPa. The much higher settlement reduction and stronger cavitation in FSW at 23 kHz suggest that cavitation is a possible if not most likely mechanism for the cyprid inhibition. The cavitation induced force may lead to physical damage to the cyprids which subsequently will result in much higher mortality. The cavitation effect was proven to be stronger at 23 kHz than the other two frequencies with the same acoustic energy, which might explain the enhanced efficiency on settlement reduction at this frequency.