The investigations on the removal of ibuprofen (IBU) in a hybrid system coupling ozonation and nanofiltration with functionalized catalytic ceramic membrane are presented. The gaseous ozone into feed water in concentration of 11 g Nm−3was supplied. Positive influence of catalytic ozonation on ibuprofen decomposition was observed. The application of catalytic nanofiltration membrane led to the ibuprofen removal of 91% after the first 15 min from the beginning of the O3/NF process, while at the same time, for the pristine membrane, it was equal to 76%. The investigations revealed incomplete degradation of drug under pH 3 after 2 h, i.e., 89%. On the other hand, the addition of inorganic salts did not affect the catalytic ibuprofen removal efficiency. Under acidic pH, the highest permeate flux decline (26%) was noted, whereas no differences between permeate flux measured under natural and alkaline conditions were observed. During the treatment process, three IBU by-products were detected, which significantly affected the permeate toxicity; however, after 2 h of catalytic nanofiltration, the product of treatment process was found as non-toxic.