Abstract Context Large near-natural rivers have become rare in Europe, a fact reflected in the high conservation status of many riverine ecosystems. While the Balkan still harbors several intact river corridors, most of these are under pressure from planned hydropower constructions. Unfortunately, there is little information available on the hydromorphodynamics and biota of Balkan rivers under threat. Objectives We present a synthesis of research on the Vjosa in Southern Albania. Here, longitudinal continuity in water flow, undisturbed sediment transport and intact fluvial dynamics are still maintained, but threatened by two large dams planned in its downstream section. We intend to provide a first multidisciplinary inventory of this river system as an example of the knowledge base required for sound water management decisions in the Balkans. Methods Based on field work of a multidisciplinary consortium of scientists from Albania and other countries conducted from 2017 onwards, we summarize the most important findings on geomorphology of the riverine landscape, habitat turnover rates, vegetation ecology and selected animal taxa. Results We found evidence that significant areas (86%) of the river corridor are covered by habitats listed in Annex 1 of the European Union Habitats Directive. These are associated with a high number of threatened biota. Conclusions Our findings underscore the value of the Vjosa as one of the few remaining reference sites for dynamic floodplains in Europe and as a natural laboratory for interdisciplinary research. We emphasize that such multidisciplinary studies are a prerequisite for informed evaluation of potential impacts caused by hydropower plants.