Robotic systems evolving in hazardous and harsh environment are prone to mission failure or system loss in presence of faults. This paper presents a fault tolerant methodology, implemented into a control architecture of an underwater robot that executes biological monitoring missions. High level constraint violations (mission, safety, energy, time and localization) and low level faults (software and hardware faults) are considered using a method based on fault trees. These undesirable events are detected and treated by a fault tolerant module that decides to recover at low level or to give a feedback to the mission manager which selects the high level reaction. This fault tolerant architecture has been tested on real field conditions, and we illustrate our methodology on a set of selected events. We conclude about reliability improvement of low cost underwater robots for complex and long missions.