A separator scrubber (58) and isolation loop (78) decontaminates a fuel reactant stream of a fuel cell (12). Water passes over surfaces of an ammonia dissolving means (61) within the scrubber (58) while the fuel reactant stream simultaneously passes over the surfaces to remove contaminants from the fuel reactant into the water. An accumulator (68) collects the separated contaminants and water, and an isolation loop pump (84) directs flow of the separated contaminant stream through the isolation loop (78). A heat exchanger (86) and an ion exchange bed (88) modify the heat of, and remove contaminants from, the separated contaminant stream, and the isolation loop (78) directs the decontaminated stream back onto the packed bed (62)-. Separating contaminants from the fuel reactant stream and then isolating and concentrating the separated contaminants within the ion exchange bed (88) minimizes cost and maintenance requirements.