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This paper investigates the performances analysis of PV-RO desalination system under uniform and non-uniform irradiance conditions. The main objective is the application of Extremum Seeking Control (ESC) to the GPV side in order to overcome the generated power and water quantity losses to improve the performance of the whole system. The technical design of the developed system is based on an existing RO desalination unit beside that real climatic data taken from a local mast are involved in this study. The modeling of the whole system and the control techniques adopted in this study are fully formulated. The whole system is modeled and controlled using MATLAB/Simulink. Different scenarios (healthy and shaded) based on real climatic data have been used to carry out the results. The ESC used shows its effectiveness to extract maximum power under shaded conditions for all the proposed scenarios. Compared with conventional controllers, this technique can offer extra power surrounding 685W in several cases. Furthermore, the shading conditions can affect widely freshwater production whose losses are estimated at around 82.91% for critical scenarios. The findings results are very significant for industrialists working in this field.