Atmospheric emissions from ships are a serious environmental problem, particularly in coastal areas and port cities. Notably, sulphur dioxide (SO2) and nitrogen oxide (NOx) emissions are expected to exceed those of all land-based sources in the EU by 2020. Sulfate and nitrate particles along with emissions of primary particles (such as soot and dust) result in fine particles i.e. PM10 (particles of 10 micrometres or less), PM2.5 (particles of 10 micrometers or less) which can harm human health. The bulk of emissions on inland waterways are generated by medium to large vessels. The use of fuel cells to power those ships in the range of 300 to 600 kW would be a zero emission solution. However, the available fuel cell technology for submarines is too costly and its use in small vessels not suitable to the targeted power requirements. The task for this project was to provide a technical solution that would be scalable to typical power requirements and which could be fully integrated into surface vessels of different sizes.