The present study aims at utilizing the waste energy from a regenerative gas turbine cycle (GTC) for the production of hydrogen in a proton exchange membrane electrolysis unit (PEMEU), freshwater in a reverse osmosis desalination unit (RODU), and hot steam in a heat recovery steam generator (HRSG). The waste heat of the GTC is first recuperated in a partial cooling supercritical CO2 Brayton cycle (SCBC) to supply the required electricity for the PEMEU and RODU. Then, the residual heat is recuperated in the HRSG to produce hot steam. The waste heat of the SCBC is recovered by two thermoelectric generators in the heat dissipation stages of the cycle. The system is assessed and optimized from thermodynamic, economic, and environmental aspects for the two cases of utilizing methane and biogas as fuel. The optimization results indicate that biogas is superior from an economic aspect as the unit cost of polygeneration and economic cost rate in the case of biogas are 32.5% lower than the case of methane as fuel. On the other hand, employing methane as the fuel brings about lower environmental impacts as it causes a 29% lower environmental cost rate than the case of biogas as fuel. There is quite a narrow difference between the exergy efficiency of the two cases from 40.45% in the case of biogas to 40.72% in the case of methane as fuel. Moreover, the heat loss recovery of the GTC ameliorates the exergy efficiency by 11.96% points in the biogas case.