Facing global change, inland navigation transport is a promising sustainable transport alternative to help reduce greenhouse gas emissions. However, the development of infrastructures to promote this transport modifies eco-morphological characteristics of rivers with serious risk of disturbance of their biodiversity. The NAVIDIV project gathers 10 European research institutes and investigates the effects of inland freshwater navigation and infrastructures on biodiversity across contexts and scales in order to produce adapted recommendations for waterwayscape management. We will present the results of two major studies. (i) A global systematic review of the literature allowed us to show that navigation itself most often had negative effects on non-exotic species/communities (57%), closely followed by the combination of multiple navigation factors (52%), waterway management (40%), and infrastructures (35%). We identified remaining knowledge gaps and future research directions to better understand the mechanisms driving navigation-biodiversity relationships. (ii) The analysis of a unique compilation of observational data from multiple sources at the European scale which allowed us to quantify the effects of shipping and infrastructure density on taxonomic and functional diversity of fish and aquatic macroinvertebrates. We showed that navigation intensity decreased diversity and increased the prevalence of invasive taxa. Importantly, these effects were strongly context-dependent, with adverse effects being amplified in natural areas compared to anthropized areas. Furthermore, navigation most negatively affected benthic and non-migratory taxa. NAVIDIV provides useful synthetic knowledge and guidelines to prioritize management and restoration actions considering the various human uses of waterwayscapes and the need for transboundary waterway management.