A system and method for preventing damage to a fuel cell stack resulting from impurities in the product stream from a fuel processor, such as may occur should the separation region of the fuel processor fail. The system and method include detecting the concentration of at least one component of the product 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.