Value of the Data •The data presents differences between degradation of NAF and AMP by high frequency ultrasound. The readers can recognize the structural effects, pollutants closeness to the cavitation bubble and hydrophobic character of the target antibiotics. •Data can benefit people working on treatment of wastewaters containing antibiotics. •Data can be useful for comparative purposes about elimination of antibiotics by coupling sonochemistry with iron (II) and UVC light (i.e., sono-photo-Fenton system). •Data could be useful for scaling up of the sonochemical process to treat organic pollutants in complex aqueous matrixes rich in hydrophilic components. •Data may be utilized in further experimental works and reviews on degradation of β-lactam antibiotics by advanced oxidation processes.