Hydrogen is widely considered an essential energy carrier that has the potential to accelerate the energy transition. The Netherlands does not have the resources to fulfil the expected hydrogen demand by domestically produced hydrogen. By realising hydrogen import terminals, the Port of Rotterdam can maintain its dominating position as the (renewable) energy port in North-West Europe. This study, in which the Port of Rotterdam is used as a case study, focuses on the uncertainties hampering the realisation of hydrogen import terminals. While earlier studies have been conducted on hydrogen import, we identify two research gaps: 1) the necessity to optimise the scaling of hydrogen import terminals and 2) the inclusion of hydrogen use in multiple sectors. Through a literature review, three categories of uncertainty have been identified that are often present in hydrogen systems; economic, technical, and geopolitical uncertainties. The categories of uncertainty have been used as a guideline to identify uncertainty present in assessing the integrated hydrogen system in the Port of Rotterdam. A model that represents this system has been developed in Linny-R. Linny-R is a graphical specification language to solve Mixed-Integer Linear Programming problems. This model allowed us to adjust input parameters such as production capacities and prices, hydrogen demand, and infrastructural changes to study the identified uncertainties through sensitivity analyses and scenarios. The results of this research illustrate the need for hydrogen import to meet the projected hydrogen demand. However, hydrogen import is not cost-competitive compared to domestically produced hydrogen. This study highlights the potential to reduce costs in the production, conversion to the carrier, and shipping stage of the supply chain. Currently, Ammonia (NH3) is the cheapest hydrogen carrier followed by Liquid Organic Hydrogen Carrier (LOHC), and Liquid hydrogen (LH2). Long-term contracts are required to manage the hydrogen import transactions to resolve economic uncertainty. Technical uncertainty relates to the scaling of hydrogen import terminals and the end-user sectors’ preferences for a specific hydrogen carrier. Based on the technical characteristics of the three hydrogen carriers, LH2 shows the highest potential to supply all end-user sectors. However, LOHC and NH3 also have advantages in specific areas. Moreover, the early stage of development in LH2-technology fuels the need for LOHC and NH3, leaving the debate on which hydrogen carrier is preferred open. Furthermore, the scaling of hydrogen import terminals is complicated by the presence of salt-caverns in the northern part of The Netherlands because they provide a cheap alternative for large-scale hydrogen storage. Geopolitical uncertainties related to the hydrogen import supply chain processes are highly dependent on the production capabilities in the export countries and the distance of those countries to the Port of Rotterdam. Additionally, other nearby located ports can also realise import terminals, attracting hydrogen import, diminishing the potential dominant position of the Port of Rotterdam. However, a first-mover position could manifest the Port of Rotterdam as a dominant player in the global hydrogen market. More generally, hydrogen import terminals could provide security against geopolitical forces as it safeguards the diversity of the Dutch energy mix. We identified several avenues for future research. First, researchers interested in expanding the model’s functionalities could focus on 1) modelling a variable renewable electricity price, 2) including salt-caverns and specific hydrogen export, 3) adjusting our model by allowing only filled vessels to arrive, 4) including the Willingness To Pay (WTP) of various end-user sectors, 5) applying a method that allows the investigation of numerous possible futures. A more general recommendation is to add a new model to analyse investments and support companies’ business cases by integrating hydrogen end-user sectors’ WTP. Finally, we especially encourage policymakers to explore and support the possibility to realise one or more hydrogen import terminals, even in case of a lacking business case, to improve the strategic position of the Port of Rotterdam with regards to economic and geopolitical advantages.