The imperative of quality and productivity has increased the complexity of technological processes, posing the problem of reliability. Today, fault diagnosis remains a very important task because of its essential role in improving reliability, but also in minimizing the harmful consequences that can be catastrophic for the safety of equipment and people. Indeed, an effective diagnosis not only improves reliability, but also reduces maintenance costs. Systems in which dynamic behaviour evolves as a function of the interaction between continuous dynamics and discrete dynamics, present in the system, are called hybrid systems. The goal is to develop monitoring and diagnostic procedures to the highest level of control to ensure safety, reliability and availability objectives. This article presents an approach to the diagnosis of hybrid systems using hybrid automata and neural-fuzzy system. The use of the neural-fuzzy system allows modeling the continuous behaviour of the system. On the other hand, the hybrid automata gives a perfect estimate of the discrete events and make it possible to execute a fault detection algorithm mainly consists of classifying the appeared defects. On the implementation plan, the results were applied in a water desalination plant.