An integrated contaminant separator and water-control loop (10) decontaminates a fuel reactant stream of a fuel cell (12). Water passes over surfaces of an ammonia dissolving means (61) within a separator scrubber (58) while the fuel reactant stream simultaneously passes over the surfaces to dissolve contaminants from the fuel reactant stream into the water. An accumulator (68) collects the separated contaminant stream, and ion exchange material (69) integrated within the accumulator removes contaminants from the stream. A water-control pump (84) directs flow of a de-contaminated water stream from the accumulator (68) through a water-control loop (78) having a heat exchanger (86) and back onto the scrubber (58) to flow over the packed bed (62). Separating contaminants from the fuel reactant stream and then isolating and concentrating the separated contaminants within the ion exchange material (69) minimizes cost and maintenance requirements.