•A novel rotation generator of hydrodynamic cavitation is presented.•Hydrodynamic cavitation has a good potential for efficient removal of pharmaceuticals.•Temperature and addition of hydrogen peroxide are important by removal process. Nowadays, due to lack of freshwater resources a sufficient wastewater management is an environmental concern. This global issue is resulting in the rapid growth of technologies for wastewater treatment. In this study a novel rotation generator of hydrodynamic cavitation is presented, which is used as a tool for pharmaceuticals removal in water. On presented machine analysis of hydrodynamics is made, where the extent and aggressiveness of cavitation is evaluated. The study has shown, that for a sufficient treatment, hydrodynamic cavitation with combination of hydrogen peroxide is needed. The removal of four pharmaceuticals (ibuprofen, ketoprofen, carbamazepine and diclofenac) was considered, where the over 80% effect was achieved. Various operating parameters such as the rotors geometry of the cavitation generator, pressure in the treatment chamber, temperature of the liquid, amount of hydrogen peroxide and time of exposure to the cavitation was investigated. The experimental results show that hydrodynamic cavitation has a good potential for efficient removal of pharmaceuticals what suggests to continue with research in this field and to consider an appropriate design for a commercial use.