In a non-interconnected area, a water-energy microgrid with distributed energy (e.g., solar panels, wind turbines, combined heat power, generators, batteries) and water resources (e.g., desalination plant, atmospheric water generator, water storage tank) could serve the demand of a discrete geographic footprint (i.e., a small town). This paper proposes an optimal management model of this type of microgrids under the minimum operation cost goal. The mathematical formulation is presented in detail, which involves constraints related to the operation of the system over a time horizon of a week. The proposed model is validated using an estimation of the water-energy demand of a generic small town located in La Guajira Department of Colombia, which is known as Ranchería. The numerical results show the effectiveness of the management model under four study cases.