We attempted to develop green nanoemulsions (ENE1−ENE5) using capryol-C90 (C90), lecithin, Tween 80, and N-methyl-2-pyrrolidone (NMP). HSPiP software and experimentally obtained data were used to explore excipients. ENE1−ENE5 nanoemulsions were prepared and evaluated for in vitro characterization parameters. An HSPiP based QSAR (quantitative structure−activity relationship) module established a predictive correlation between the Hansen solubility parameter (HSP) and thermodynamic parameters. A thermodynamic stability study was conducted under stress conditions of temperature (from −21 to 45 °C) and centrifugation. ENE1−ENE5 were investigated for the influence of size, viscosity, composition, and exposure time on emulsification (5−15 min) on %RE (percent removal efficiency). Eventually, the treated water was evaluated for the absence of the drug using electron microscopy and optical emission spectroscopy. HSPiP program predicted excipients and established the relationship between enoxacin (ENO) and excipients in the QSAR module. The stable green nanoemulsions ENE−ENE5 possessed the globular size range of 61−189 nm, polydispersity index (PDI) of 0.1−0.53, viscosity of 87−237 cP, and ζ potential from −22.1 to −30.8 mV. The values of %RE depended upon the composition, globular size, viscosity, and exposure time. ENE5 showed %RE value as 99.5 ± 9.2% at 15 min of exposure time, which may be due to the available maximized adsorption surface. SEM-EDX (scanning electron microscopy−X-ray dispersive energy mode) and inductively coupled plasma−optical emission spectroscopy (ICP-OES) negated the presence of ENO in the treated water. These variables were critical factors for efficient removal of ENO during water treatment process design. Thus, the optimized nanoemulsion can be a promising approach to treat water contaminated with ENO (a potential pharmaceutical antibiotics).