The introduction of pharmaceuticals into aquatic ecosystems can lead to the generation of antibiotic-resistant bacteria. This paper employed molecular dynamics simulations to examine the interactions between cationic/anionic surfactants and two antibiotics or drugs, namely, ciprofloxacin and azithromycin. The analysis focused on many factors to elucidate the mechanism by which the surfactant bilayer molecular structure affects the selected antibiotics. These factors include the tilt angle, rotational angle of the surfactants, electrostatic potential, and charge density along the bilayers. Our molecular-level investigation of the adsorption mechanisms of hydrophobic (azithromycin) and hydrophilic (ciprofloxacin) drugs on the cationic/anionic surfactant bilayer offers a crucial understanding for comprehending the optimal selection of surfactants for effectively separating antibiotics.