Antibiotic contamination in aquatic environments threatens public health and ecological balance. This study introduces a novel nanocomposite by impregnating graphene oxide (GO) with a hydrophobic deep eutectic solvent (HDES). The novel nanocomposite was used to remove meropenem (MEM) antibiotic from aqueous solutions effectively. Ten natural HDESs were screened, and thymol:levulinic acid-impregnated GO nanocomposite GO@Thy:LevA (1:3) was the best-performing adsorbent. The successful integration of HDES into GO nanocomposite was confirmed using several characterization techniques, including X-ray diffractometer (XRD), Raman spectroscopy, Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), total organic carbon analysis (TOC), scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), transmission electron microscopy (TEM), atomic force microscopy (AFM) and and X-ray photoelectron spectroscopy (XPS). The adsorption performance of the synthesized nanocomposite adsorbents was evaluated under optimized conditions (C0 = 160 mg/L, pH = 7, mixing time = 120 min, adsorbent = 10 mg, stirring = 300 rpm, volume = 10 mL), with pristine GO and GO@Thy:LevA (1:3) nanocomposite exhibiting remarkable adsorption capacities of 63.50 mg/g and 91.51 mg/g, respectively. Kinetic studies showed that the adsorption process followed a pseudo-first-order model, whereas thermodynamic analysis confirmed the endothermic and spontaneous nature of the adsorption process. Advanced statistical physics models, particularly the monolayer model with two energies (M2), have provided new insights into the adsorption mechanism at the molecular level. Density functional theory (DFT) calculations and conductor-like screening model for real solvents (COSMO-RS) studies further elucidated the adsorbent-adsorbate interactions, with theoretical predictions corroborating experimental findings. The reusability of the adsorbents over five cycles was demonstrated, highlighting their potential for practical applications.