Water management in a PEMFC stack was studied, using a specially developed EIS spectrometer. A 25-1 fractional factorial test plan was used to define operating conditions. Studied factors were: reactant overstoichiometric ratio and inlet reactant relative humidity in both compartments and temperature. Impedance spectra were treated by equivalent circuit and physical modelling, providing 7 responses: ohmic resistances obtained from both models, charge transfer resistance, CPE parameters, ratios between ionic and electronic conductivities and between double layer capacitance and exchange current density. Results showed that physical model has no significant added value versus an equivalent circuit analysis much more easily handled. Moreover, only two responses are relevant for diagnostic purpose: ohmic and charge transfer resistances. Cathodic gas over-stoichiometry and inlet relative humidity represent for ~45% of total effects on both responses. But, other factors and interactions are impacting the responses differently, paving the way for the development of a diagnostic algorithm.