The Dutch inland shipping sector aims to nearly eliminate emissions by 2050 by transitioning away from fossil fuels. While alternative fuels are being developed, scaling them up remains challenging due to complex system dynamics, often leading to innovation failure. Existing studies identify scale-up factors but often overlook interactions between factors. This study examines the scale-up dynamics of biofuels, hydrogen and LNG. Scientific literature, news articles and interviews are analysed to construct causal loop diagrams depicting the main relationships between economic, technological, political and social factors. Six mechanisms showcasing scale-up dynamics are identified, highlighting the widespread impact of uncertainty–influenced by technical challenges, resource availability and fuel alternatives–and industry interest–influenced by cost–benefit assessment, technical challenges and resource availability. While biofuels, hydrogen and LNG show common mechanisms, resource availability creates key differences. A holistic approach addressing uncertainty and industry interest is needed to shift a system currently reinforcing fossil fuels.