The PEM fuel cell commercial industrialization is still hampered due to some reliability issues. Their performances are mainly affected by a poor water management. Hence, Electrochemical Impedance Spectroscopy (EIS) is used to characterise the PEMFC state-of-health and to prevent these degradations. In the present work, a diagnostic tool has been developed. A PEMFC test station, up to 2,4 kW, has been designed to run EIS experiments under controlled operating conditions (pressure, reactants mass flow rate, temperature and hygrometry). A 400 W electrical output stack (16 cells) is used where every cell is monitored. Cell impedance measurements are analysed thanks to an original pseudo 2D modelling based on fundamental fuel cell equations describing charges and species transport, electrochemical reactions. The computed cell frequency response is fitted on impedance measurement and intrinsic physical fuel cell parameters are identified. These parameters are then used to determine the stack state- of-health cell by cell and to discriminate the contribution of each phenomenon on cell degradations. The developed diagnostic tool is able to detect oxygen starvation due to cell flooding before it gets critical. Moreover, it has been shown that stack flooding conditions lead to cell heterogeneities where cell flooding and drying may appear at the same time through the stack.