A transient 2D physical continuum-level model for analyzing polymer electrolyte membrane fuel cell (PEMFC) performance is developed and implemented into the new numerical framework NEOPARD-X. The model incorporates non-isothermal, compositional multiphase flow in both electrodes coupled to transport of water, protons and dissolved gaseous species in the polymer electrolyte membrane (PEM). Ionic and electrical charge transport is considered and a detailed model for the oxygen reduction reaction (ORR) combined with models for platinum oxide formation and oxygen transport in the ionomer thin-films of the catalyst layers (CLs) is applied. The model is validated by performance curves and impedance spectroscopic experiments, performed under various operating conditions, with a single set of parameters and used to study water management in co-and counter-flow operation. Based on electrochemical impedance spectra (EIS) simulations, the physical processes which govern the PEMFC performance are analyzed in detail. It is concluded that the contribution of diffusion through the porous electrodes to the overall cell impedance is minor, but concentration gradients along the channel have a strong impact. Inductive phenomena at low frequencies are identified from physics-based modeling. Induction is caused by humidity dependent ionomer properties and platinum oxide formation on the catalyst surface.