Bond graphs are a promising possibility for modeling complex physical systems. This paper explores its potential by undertaking the analysis, modeling and design of a water pumping photovoltaic system. The effectiveness of photovoltaic water pumping systems depends on the sufficiency between the generated energy and the volume of pumped water. Another point developed in this paper presents the optimization of a photovoltaic (PV) water pumping system using maximum power point tracking technique (MPPT). The optimization is based on the detection of the optimal power. This optimization technique is developed to optimize the usage of power. The presented MPPT technique is used in photovoltaic water pumping system in order to increasing its efficiency. A buck–boost chopper allows an adaptation interface between the panel and the battery checked by a tracking mechanism known as the MPPT (Maximum Power Point Tracking). A new algorithm is presented to control a maximum power point tracker MPPT through a bond graph. From the chemical reactions in the batteries to the control laws of the power electronics structures, a bond graph model is proposed for every single part of the system. The model is used in simulations and the results compared to actual measurements. The model is used in simulations and the results compared to actual measurements, showing an accuracy of nearly 99%.