The widespread use of synthetic drugs and as feed additives has resulted in the release of large amounts of biologically active chemicals into the environment. Exposure to environmentally relevant concentrations of chemicals can have severe effects on human health. Therefore, effective degradation of these synthetic, biologically active compounds is of paramount importance. Diphenhydramine (DPH) has been selected as a target compound for ultrasound remediation. The results demonstrated that ultrasound-induced degradation has potential applications in managing aqueous media contaminated with DPH. Atorvastatin and roxarsone have been selected as representative substrates for chloroperoxidase (CPO) catalyzed transformation of pollutants. These studies demonstrate atorvastatin and roxarsone can be degraded efficiently by CPO. The transformation products of each compound were identified and the mechanisms of CPO catalysis postulated. This study provides a foundation for assessing the feasibility of applying CPO in the remediation of water and soil contaminated with pharmaceuticals and feed additives.