A novel polymer synthesized by grafting three cyclodextrins onto chitosan was characterized and evaluated for its potential to adsorb two pharmaceutical residues: ibuprofen and progesterone. The influence of various operational parameters, including contact time, initial molecule concentration, pH, ionic strength, and temperature, was investigated. The synthesized polymer exhibits an amorphous and porous structure with a remarkable swelling capacity of 9.5 mmol/g. It demonstrates remarkable adsorption capacities for progesterone and ibuprofen, reaching 90% and 75%, respectively. Kinetic studies reveal that the adsorption of both molecules follows a pseudo-second-order model. A DSC analysis elucidated the adsorption mechanism, which is governed by the formation of inclusion complexes and electrostatic interactions within the polymer network. The polymer’s regeneration after 23 cycles demonstrates its sustainable adsorption efficiency. The combination of chitosan with three cyclodextrins opens up promising new avenues for water treatment and the removal of specific pollutants. This approach significantly improves the material’s selectivity towards target pollutants, offering a significant advantage in pollution remediation applications.