Considering water molecules as a whole anisotropic medium, and not as a collection of isolated molecules, is critical to model faithfully the complex water interactions. The Wa-terKit protocol shows that by modeling rather simple rules and opportune sampling it is possible to generate thermodynamically meaningful ensembles that can approximate with rather good accuracy the interactions between water molecules and proteins. WaterKit can rapidly provides accurate predictions for both placement of individual water molecules and the associated free energy estimates.