We report on the effectiveness of sonication on controlling the growth of four problematic algal species which are morphologically different and from three algal divisions. Two cyanobacterial species Microcystis aeruginosa (unicellular) and Aphanizomenon flos-aquae (filamentous), one green alga Scenedesmus subspicatus (colonial) and lastly a diatom species Melosira sp. (filamentous) were subjected to ultrasound of selected low to high frequencies ranging from 20 to 1144 kHz. Microcystis aeruginosa and Scenedesmus subspicatus highest cell removal rates were 16±2% and 20±3% when treated with the same ultrasound frequency of 862 kHz but differing energy levels of 133 and 67 kWh m−3, respectively. Aphanizomenon flos-aquae best removal rate was 99±1% after 862 kHz and 133 kWh m−3 of energy, with Melosira sp. achieving its highest cell removal at 83% subsequent to ultrasound of 20 kHz and 19 kWh m−3. Microcystis aeruginosa and Scenedesmus subspicatus are considered non-susceptible species to ultrasound treatment from a water treatment perspective due to their low cell removal rates; however, photosynthetic activity reduction of 65% for Microcystis aeruginosa does indicate the possible utilization of ultrasound to control bloom growth, rather than bloom elimination. Conversely, Aphanizomenon flos-aquae and Melosira sp. are deemed species highly susceptible to ultrasound. Morphological differences in shape (filamentous/non-filamentous) and cell wall structure (silica/peptidoglycan), and presence of gas vacuoles are probable reasons for these differing levels of susceptibility to ultrasound.