Pharmaceutical pollutants in hospital wastewater (HWW) have the potential to contaminate both aquatic and terrestrial natural environments, posing a threat to aquatic life and human health. This work aimed to screen some chemical pollutants in HWW and evaluate the capacity of two magnetic nanocomposites (Fe₃O₄@SiO₂ and NiFe₂O₄ NCs) to remove these pollutants from HWW. The manufactured nanocomposites were described with different techniques. The collected HWW samples were screened by LCMS/ MS and HPLC/ UV before and after treatment to detect the capacity of certain pharmaceutical pollutants. The screening results of HWW showed that numerous different compounds belonging to diverse groups of drugs were found in the water samples. Both nanocomposites exhibited a significant activity in degradation, removing a high concentration of the pharmaceutical pollutants in treated HWW. Meanwhile,  data based on HPLC/ UV analysis revealed that, NiFe₂O₄ NC was more effective than Fe₃O₄@SiO₂ NC, which removed more peaks of several selected compounds, indicating its capacity to reduce these pollutants. Therefore, the outcomes of the current research provided new innovative effective materials for treating hospital wastewater, which can contribute to preventing the spread of pollutants and preserving the aquatic environment.