The simultaneous removal of two or more pollutants from an aqueous medium requires a composite adsorbent that can provide sites specific to different adsorbates. But it is difficult to decipher the molecular-level adsorption mechanism under such circumstances. We combine experimental and classical molecular dynamics simulations to gain insight into this research problem. The present research investigates the simultaneous removal of ciprofloxacin (CIP) and methyl orange (MO) from an aqueous medium using a composite of graphene oxide (GO) and superparamagnetic NiFe2O4 nanoparticles. The adsorbent demonstrated economical and efficient magnetic recyclability. The co-adsorption isotherm data for CIP and MO best fitted the Extended Freundlich model, in agreement with the heterogeneous adsorption sites available on the composite. The experimental results were combined with classical molecular dynamics simulations to understand the predominant molecular-level adsorbate-adsorbent interactions. The latter revealed the two adsorbates adsorb to distinctly different adsorption sites on the NiFe2O4/GO composite.