A fluidized 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 media (61) within a fluidized bed (62) while the fuel reactant stream simultaneously passes over the surfaces to dissolve contaminants from the fuel reactant stream into a separated contaminant and water stream. A fuel-control heat exchanger (57) upstream from the scrubber (58) removes heat from the fuel stream. A water-control loop (78) directs flow of the separated contaminants and water stream from an accumulator (68) through an ion exchange bed (88) which removes contaminants from the stream. Decontaminated water is directed back into the scrubber (58) to flow through the fluidized bed (62). Separating contaminants from the fuel reactant stream and then isolating and concentrating the separated contaminants within the ion exchange material (88) minimizes costs and maintenance requirements.