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The use of photovoltaic system especially for water pumping is one of the best alternative methods for irrigation in most rural and desert areas. However, the intermittent nature of photovoltaic energy and the limited battery lifetime remain the major impediments to the evolution of using the Photovoltaic Water Pumping System (PVWPS). This paper aims to analysis and improve the PVWPS performances for irrigation in Jerid Tunisia. In this context, the sizing of the PVWPS is investigated firstly. Then, a performances analysis of PVWPS is done with the aim to identify the critical failure modes. The improvement of PVWPS performances is ensured by the use of an appropriate charge control strategy for battery pack and the integration of a Hybrid Energy Storage System (HESS). Finally, an improved Energy Management System (EMS) for HESS is developed to ensure an adequate distribution of energy from different sources. The results show that the proposed charge control for battery pack and the HESS improve the PVWPS availability under critical climatic conditions as well as its reliability.