The removal of pharmaceutical residues from water resources using bio-based materials is very important for human safety and health. Bio-based graphene oxide/chitosan (GO/CS) aerogel microspheres were fabricated with emulsification and cross-linking, followed by freeze drying, and were used for the adsorption of levofloxacin (LOF). The obtained GO/CS aerogel microspheres were characterized with scanning electron microscopy (SEM), Fourier-transform infrared (FTIR), and thermogravimetry (TG). The effects of GO content, pH value, and temperature on their adsorption capacity were investigated. With the incorporation of 40 wt% GO, the adsorption capacity increased from 9.9 to 45.6 mg/g, and the highest adsorption capacity, 51.5 mg/g, was obtained at pH = 8 and T = 25 °C. In addition, to obtain deeper insight into the adsorption process, the thermodynamics and kinetics of the process were also investigated with four different models of LOF adsorption. The thermodynamic modeling results revealed that LOF adsorption is exothermic, and the kinetic investigation demonstrated that LOF adsorption is generally consistent with a pseudo-first-order rate law.