Natural river landscapes can be biodiversity hotspots but are one of the most human altered ecosystems with habitats significantly damaged around the world, and a third of fish populations threatened with extinction. While riparian ecosystems have been negatively altered by anthropogenic activities, effective planning and restoration strategies can reverse negative impacts by improving habitat quality. However, restoring rivers requires appropriate data on current riparian health while also considering priorities for different stakeholders. To address this, a Geographic Information System (GIS) was used to create a new and transferable restoration priority model based on a section of the river Linth in Switzerland as a case study. The restoration priority model is founded on connectivity, river condition, national priority species and species hotspots. Landscape change of the riparian zone was analyzed using aerial imagery and landscape metrics. Almost a quarter of rivers within the study area were considered high or very high restoration priority, with many aquatic species set to benefit from restoration. From 1946 to 2019, the riparian landscape became highly fragmented due to significant growth in impervious surfaces and a concomitant loss of agricultural land. The GIS model provides a tool by which environmental agencies can manage natural features over large scales, while also planning priorities and targeting conservation strategies to the areas of greatest need.