The CCNR will ensure that in 2050 inland ships do not emit any emissions. A PEM fuel cell system running on pure hydrogen could be a solution. However, the new system imposes some difficulties on the design of the inland ship. A calculation model is created to evaluate inland ships with this system and research these difficulties. The calculations are performed for shallow water. An elaboration is given on the design implications to incorporate their effects in the calculations. The inland ships are eventually judged base on their required freight rates. This research concludes the high hydrogen fuel price results in a lower optimal ship speed and a higher required freight rate than those of a conventional inland ship. Furthermore, increasing the installed power or increasing the refuelling frequency can improve the required freight rate.