A unique, generic, transient, and more general PEMFC contamination model able to predict the cell performance impact of foreign cations exchanging with ionomer protons was derived by adding a variable equivalent proton fraction in the flow field channel liquid water drops. Ion exchange phenomena are described with appropriate and recognized relationships. Steady state ohmic performance losses and time constants for both contamination and recovery processes were used to define contaminant tolerance limits for monovalent, divalent and trivalent cations and are respectively equal to 5100, 380 and 4.4 ppm. These tolerance limits are expected to be widely applicable for similarly charged cations because model parameters, ionic conductivity and separation factor, do not vary significantly (first order approximation). The model also describes the effect of ammonia, revealing that its fast reaction with ionomer protons creating ammonium ions at the gas phase/membrane phase boundary is analogous to ion exchange. A 2.1 ppb tolerance limit is proposed which does not take into account the scavenging effect of liquid water (parallel contamination path). The model applicability to ammonia enlarges the existing contamination model library specifically developed to facilitate mechanism identification (fingerprinting) and addresses the large number of untested and unidentified contaminants.