Many analyses have been completed on the operating characteristics of fuel processors as a function of fuel usage, power density and specific power as related to efficiency. In addition, it is widely recognized that depending on the fuel type, fuel processors will either be net producers or consumers of water. This has led to theoretical simulations to determine the maximum efficiency that can be achieved given a processor's overall water balance. Moreover, the effect of water for steam and autothermal reformers (ATR) has been investigated to gain an understanding of how it will be influenced given the net results of the system water balance. However, little attention has been given to the effect of water on the reactors downstream of the reformer. Furthermore, a simulation that incorporates the actual, not only theoretical, operation of the reactors coupled with the water balance issues has not been investigated until now. This paper will report on the effect of water on the operation of the CO clean-up train. including water-gas-shift (WGS) and preferential oxidation (PROX) reactors, and its influence on the overall efficiency of the processor system as compared to theoretical thermodynamic calculations. The comparison illustrates that a purely thermodynamic simulation can lead to a less efficient system design than could otherwise be possible once actual reactor performance is included. (c) 2004 Elsevier B.V. All rights reserved.