Pumping water using multiple energy sources is the ideal solution for supplying of potable water in isolated or arid areas. In this paper, an effective control and energy management strategy for a stand-alone photovoltaic-batteries water pumping system for agriculture applications is presented. The system is composed of photovoltaic solar panels as primary energy sources, and Lead-Acid batteries as seconder energy sources to supply the brushless DC motor and the centrifugal pump. The energy management strategy uses an intelligent algorithm to satisfy the energy demanded by the motor, also to maintain the state-of-charge of the battery between safe margins in order to eliminate the full discharge and the destruction of the batteries. Drift is a major problem in photovoltaic systems; this phenomenon occurs when the solar irradiation changes rapidly. Classical MPPT algorithms do not solve this problem, for this reason a modified P&O has been implemented, the obtained results shown the efficiency of the algorithm compared to the conventional P&O. Computer simulation results confirm the effectiveness of the proposed energy management algorithm under random meteorological conditions.