This study introduces a novel method for controlling an autonomous photovoltaic pumping system by integrating a Maximum Power Point Tracking (MPPT) control scheme with variable structure Sliding Mode Control (SMC) alongside Perturb and Observe (P&O) algorithms. The stability of the proposed SMC method is rigorously analyzed using Lyapunov’s theory. Through simulation-based comparisons, the efficacy of the SMC controller is demonstrated against traditional P&O methods. Additionally, the SMC-based system is experimentally implemented in real time using dSPACE DSP1104, showcasing its robustness in the presence of internal and external disturbances. Robustness tests reveal that the SMC controller effectively tracks Maximum Power Points (MMPs) despite significant variations in load and solar irradiation, maintaining optimal performance even under challenging conditions. The results indicate that the SMC system can achieve up to a 70% increase in water flow rates compared with systems without MPPT controllers. Furthermore, SMC demonstrated high sensitivity to sudden changes in environmental conditions, ensuring efficient power extraction from the photovoltaic panels. This study highlights the advantages of integrating SMC into Photovoltaic Water Pumping Systems (PV-WPSs), providing enhanced control capabilities and optimizing system performance. The findings contribute to the development of sustainable water supply solutions, particularly in remote areas with limited access to the electrical grid.