Substances such as pharmaceuticals, pesticides, dyes, synthetic and natural hormones, plasticizers, and industrial chemicals enter the environment daily. Many of them are a matter of growing concern worldwide. The use of ultrasound to eliminate these compounds arises as an interesting alternative for treating mineral water, seawater, and urine. Thereby, this work presents a systematic and critical review of the literature on the elimination of organic contaminants in these particular matrices, using ultrasound-based processes. The degradation efficiency of the sonochemical systems, the influence of the nature of the pollutant (volatile, hydrophobic, or hydrophilic character), matrix effects (enhancement or detrimental ability compared to pure water), and the role of the contaminant concentration were considered. The combinations of ultrasound with other degradation processes, to overcome the intrinsic limitations of the sonochemical process, were considered. Also, energy consumptions and energy costs associated with pollutants degradation in the target matrices were estimated. Moreover, the gaps that should be developed in future works, on the sonodegradation of organic contaminants in mineral water, seawater, and urine, were discussed.