Pharmaceutical contaminations in the water resources becomes very serious global environmental issue. Therefore, these pharmaceutical molecules should be removed from the water resources. In the current work, 3D/3D/2D-Co3O4/TiO2/rGO nanostructures were synthesized through a facile self-assembly-assisted solvothermal method for an effective removal of pharmaceutical contaminations. The nanocomposite was finely optimized through the response surface methodology (RSM) technique with different initial reaction parameters and different molar ratios. Various characterization techniques were used to understand the physical and chemical properties of 3D/3D/2D heterojunction and its photocatalytic performance. The degradation performance of ternary nanostructure was rapidly increased owing formation of 3D/3D/2D heterojunction nanochannels. The 2D-rGO nanosheets play an essential role in trapping photoexcited charge carriers to reduce the recombination process rapidly as confirmed by photoluminescence analysis. Tetracycline and ibuprofen were used as model carcinogen molecules to examine the degradation efficiency of Co3O4/TiO2/rGO under visible light irradiation using halogen lamp. The intermediates produced during the degradation process were studied using LC-TOF/MS analysis. The pharmaceutical molecules tetracycline and ibuprofen follows pseudo first order kinetics model. The photodegradation results show that the 6:4 M ratio of Co3O4:TiO2 with 5% rGO exhibits 12.4 times and 12.3 higher degradation ability than pristine Co3O4 nanostructures against tetracycline and ibuprofen, respectively. These results shows high efficiency of Co3O4/TiO2/rGO composite against the degradation of tetracycline and ibuprofen.