In this paper, a robust optimal efficiency controller for a complete water pumping system is designed based on the Fractional order Integral Sliding Surface (FISMC) with Linear Quadratic Regulator (LQR) related to the Minimum Electric Loss (MEL) condition. The developed model's novelty is based on a strategy to improve the control's performance robustness with optimal costs, in which a compromise is made between minimizing electric motor power losses and accurate flow rate adjustment in order to operate the pump at its best efficiency point and increase discharge flow rate stability for more flexibility against frequently changing working conditions. The whole system is simulated in MATLAB SIMULINK workspace, and a comparative analysis based on control energy, chattering phenomena, stability and control robustness has been conducted between the conventional PI, LQR, Integral Super-Twisting Sliding Mode Surface (ISTSMC) and the proposed control strategy MEL-FISMC-LQR. Finally, we evaluated the performance of the designed controls, including the Integral Absolute Error (IAE). The simulation results show that the proposed control design significantly improves pumping system efficiency and stabilizes the discharge flow rate at each operation point of the pumping system, and also improves flexibility against variable-speed and throttling valve. Furthermore, the stability of the closed-loop control system is assured by Lyapunov approach, and dynamic performance regardless of external disturbances as well as unknown uncertainties and parameter variations.