Several measures have been developed to prevent emissions from inland water transportation. However, it is challenging to weigh all the aspects to identify the pathway that will ultimately result in zero-emission inland shipping. A data-driven virtual representation of the inland shipping system can be used to evaluate zero-emission strategies, effectiveness of policies and technologies, and consequences of their implementation. This multi-level digital twin can realistically represent the system with all relevant components, which needs to be validated using real-world data. Subsequently, future scenarios can be imposed on the digital twin, and the proposed intervention measures can be applied, based on which their efficiency can be assessed together with the inland shipping sector. This study discusses the essential aspects of designing a digital twin for an IWT. Three aspects are considered essential: individual ships, logistics chains, and infrastructure. As these research topics span various scales, ranging from a single vessel to an entire infrastructure network, an agent-based approach is suitable for forming the basis of the digital twin. Consequently, potential interventions can be considered, ranging from the application of new technologies to individual vessels to policy measures implemented for an entire shipping corridor or various bunker infrastructure strategies in the network. Additionally, the impact of the implemented interventions can be evaluated at any desired scale, ranging from the individual ship level and its emissions to the network level and aggregated emissions in an entire area, or the impact on the logistics chain.