A system and method for preventing damage to a fuel cell stack resulting from impurities in a hydrogen stream delivered thereto. In some embodiments, the hydrogen stream is a product hydrogen stream from a fuel processor. In some embodiments, the impurities may result from a failure or malfunction in a separation region adapted to remove impurities in the hydrogen stream. The system and method include detecting the concentration of at least one component of the hydrogen stream and isolating the fuel cell stack should this concentration exceed an acceptable threshold level. In some embodiments, the system or method are adapted to detect the concentration of a component that itself is not harmful to the fuel cell stack, or which is not harmful in an associated threshold concentration. In some embodiments, the detected composition is at least one of water, methane, and carbon dioxide.