This paper presents an optimal design for sustainable hybrid energy systems for the aquaculture sector, which inherently requires intensive energy. The designed system is energized by renewable resources to produce pure oxygen in situ through water electrolysis for oxygenation according to the changes of dissolved oxygen of species under culture. Moreover, the by-product hydrogen from the electrolysis process is used to generate backup power for an eventual power failure. The mathematical models of the system were developed for simulation and optimization to assess the performance of the system regarding technical, economic, and environmental aspects as multi-objective functions in autonomous mode as well as on-grid mode. The merits of the proposed system are demonstrated at a shrimp farm. Furthermore, the optimal results and their sensitivity analysis showed that the sustainable hybrid energy system operating in grid-connected mode, which possesses such attractive features as producing onsite pure oxygen for oxygenation and utilizing the by-product hydrogen for generating backup power, could bring significant benefits for farmers thanks to a notable reduction in the annualized cost of the system as well as CO2 emission in comparison with the conventional system, which is powered by the national grid to run common paddlewheel aerators for oxygenation.