In this paper, a novel electricity and freshwater cogeneration system is proposed in which an organic Rankine cycle (ORC) is utilized for recovering the wasted heat of a Solid Oxide Fuel Cell (SOFC). The electricity generated in the recovery unit is used to derive a Reverse Osmosis (RO) water desalination unit. Also, three different configurations are considered for the ORC unit. At the first step, a robust three-objective genetic optimization is applied for all three configurations and the best one is selected to have the maximum generated power, minimum total productions cost, and minimum pollutant emissions, simultaneously. The second step is focused on selecting the best working fluid of the optimal ORC (among five different working fluids). The results demonstrated that the regenerative configuration with the R123 working fluid has the best performance. For this optimal layout, the outputs are included 649.2 kW of the net generated power and 34.5 m3/h of freshwater At this condition, the optimal exergy efficiency, product unit cost, and pollutant emission factor are 46.29%, 28.59 US$/GJ, 0.2587 kg/kWh, respectively.