In this work, we successfully implemented a separation of states protocol to compute RBFEs for ligand pairs, where in each ligand pair, one ligand binds to the target protein with a trapped water while the other ligand displaces it. In our RBFE protocol, we implemented harmonic position restraint on the trapped water, a solvent repulsion term, and position restraints on the binding site. We calculated RBFEs for five ligand pairs and our calculations resulted in errors within 0.7 kcal mol -1 . Our calculated RBFE values are largely in agreement with literature values. Our RBFE protocol is an extension of a separation of states based ABFE protocol for trapped waters' decoupling from proteins/protein-ligand complexes, first studied by Ge et al. and further optimized in this study.