This study focuses on ultrasonic-assisted cleaning of MD membranes for the treatment of high-TDS feed waters. The conditions for the ultrasonic application were explored to increase the cleaning efficiency and to minimize physical damage to the membrane. MD fouling tests were performed using synthetic feed waters with high scaling potential. After the fouling tests, cleaning experiments were performed by immersing the membrane cell in an ultrasonic generator and operated with a citric acid solution. The recovery of membrane permeability, liquid entry pressure, and ion rejection were measured, and scanning electron microscopy was used to visually analyze the membrane surface. Results indicated that the ultrasonic irradiation at low frequencies (28 and 45 kHz) led to either structural damage or wetting of the MD membranes. However, the ultrasonic irradiation at a higher frequency (72 kHz) exhibited a high cleaning efficiency without the structural damage and wetting. Compared with physical and chemical cleaning techniques, the ultrasonic-assisted cleaning resulted in higher flux recovery and foulant removal with a reduction in cleaning chemical consumption.