Inland waterways and their connections to marine transport systems constitute a substantial resource for the establishment of green infrastructures, flood prevention, and environmental conservation. However, these developments have numerous inherent environmental hazards such as water and air pollution, a loss of habitats, increased coastal erosion, the transfer of invasive species between connected watercourses and lakes, and the transport of pollutants through watercourses to coastal areas. Climate change may aggravate these environmental problems through changing temperatures, reduced precipitation, enhancing the adverse impact of excess nutrient discharge, and the entry of invasive species. In this study, we analyse the main European inland waterway corridors and their branches to assess the ecological viability of a pan-European inland waterway network. The environmental viability of such network depends on the right assessment of ecosystem services and protection of biodiversity. A model structure for landscape conservation, green infrastructure development, water replenishment, and ecosystem reconstruction is proposed, considering a sustainable combination of multimodal inland waterway and rail transport.