Future demand for container transport is expected to increase, placing pressure on the port-hinterland system of the Rhine river. To meet European climate goals and relieve the congested road freight system, inland waterway transport (IWT) is promoted as a sustainable alternative. However, IWT is vulnerable to low water levels as a result of climate change, as evidenced by significant drought periods in 2018. This research investigates how the strategic establishment of transshipment hubs can enhance the climate resilience of the port-hinterland system of the Rhine river under varying river discharge scenarios. The focus is on three critical bottlenecks in terms of available draught: Druten, Duisburg, and Kaub. This study quantifies the impact of new hubs on the total cost and CO2-equivalent emissions by developing a mathematical location routing model, which is used for a scenario-based analysis with varying river discharge levels and rail capacity levels. Results show that hub establishment significantly reduces both total transport costs and CO2-equivalent emissions during low discharge scenarios, without requiring expansion of existing terminals. The establishment of hubs depends on location and multimodal accessibility, with rail connections only becoming economically viable when the remaining hub-destination distance exceeds certain distance thresholds. The findings provide actionable insights for policymakers and transport authorities on strategic decisions of infrastructure investments to improve the climate-resilience of freight transport along the Rhine corridor to minimize total costs, reduce CO2-equivalent emissions, and relieve congested road networks.