Application of PV generators for water pumping applications, especially in remote area of developing countries, has received much attention. Since the output of a PV generator is essentially dc in nature, a dc motor is an obvious choice for the prime mover of the pump. This avoids the use of an inverter, which will be required to drive the induction motor in case the conventional water pumping systems is chosen. The dc motor option gives better overall efficiency for low power applications. Therefore, for low power applications dc motors are preferred in spite of maintenance problem. In this work MATLAB /SIMULINK software is used for modeling PV cell which is further modified to develop a PV array model. Simulation model was also developed for PV based water pumping system and the performance of the system is analyzed with various configurations of PV array.