The discharge of toxic metal ions and pharmaceutical pollutants has become a global issue. This work evaluated the efficiency of the hydrothermally synthesized superparamagnetic Fe3O4-MoS2 nanosheets and its fabrication with chitosan (Fe3O4-MoS2@CS) to remove Cr(VI) and ciprofloxacin (CIP) from simulated wastewater. These nanohybrid materials are characterized by SEM-Mapping, Raman, TEM, XRD, XPS, zeta potential, FTIR, and BET analyses. The affinity and selectivity of Fe3O4-MoS2@CS nanomaterial towards a mixture of Cr(VI), As(II), Pb(II), and Cd(II) metal ions from synthetic solution is studied through ICP-MS at trace levels. The distribution coefficient (Kd) for Cr(VI) (1.2 x 104 mL/g) is higher than the other metal ions, which reveals high selectivity of Fe3O4-MoS2@CS. The Fe3O4-MoS2@CS has also displayed enhanced removal efficiency for ciprofloxacin (emerging contaminant) from synthetic solutions. The Fe3O4-MoS2 and Fe3O4-MoS2@CS nanomaterials possess high saturation magnetization values of 68.00 emu/g and 59 emu/g, respectively. The adsorption process of Cr (VI) highly depends upon the solution pH, and the adsorption isotherm is followed by the Langmuir isotherm model. The kinetics of sorption is followed well by the pseudo-second-order model. The adsorption mechanism is assumed due to functional group complexation, and electrostatic interactions. Fe3O4-MoS2@CS has displayed maximum sorption capacity for Cr(VI) (175.4 mg g-1) and CIP (190.7 mg g-1) respectively. Fe3O4-MoS2@CS has been used in practical applications to remove Cr(VI) (97 %) and CIP (62 %) from real simulated wastewater. The enhanced adsorption efficiency and excellent magnetic recyclability of Fe3O4-MoS2@CS nanohybrid material make it a promising sustainable adsorbent for clean production and wastewater treatment.