Transport phenomena of mass, energy, momentum and electrical charges play a significant role in proton exchange membrane fuel cells (PEMFCs). In this study the transport and balance equations are the basis of a simulation model which allows the evaluation of the distribution of the physico-chemical parameters within the structure of a PEMFC reactor. Model Validation is presented; the validated model is than used to investigate the behaviour of the reactor, with particular attention to critical operating conditions. Critical conditions arise in a number of cases: flooding, membrane drying and degradation due to temperature peaks are discussed in this paper.