The European Union’s Biodiversity Strategy 2030, reinforced by the new Nature Restoration Law, targets restoring a minimum of 25,000 km of ‘free-flowing rivers’ by 2030. Central to this endeavor is the imperative to restore natural longitudinal and lateral connectivity of rivers and floodplains. Focused on scrutinizing data, methods, and tools employed in published studies from 2000 to 2023, our literature review reveals both encouraging developments and significant challenges at pan-European and regional scales to prioritize barriers for removal. Positive advancements include notable efforts in (i) data collection for a diverse range of taxa, and (ii) barrier data acquisition over the past two decades. Additionally, (iii) robust prioritization algorithms have been established. However, there remain significant challenges in applying these frameworks consistently across diverse geographical regions. We identified knowledge gaps in the (iv) quality of the available data, emphasizing the need for more accurate information on barrier characteristics, (v) the lack of inclusion of social aspects, and (vi) the need for expanding the focus beyond commercially significant species. We conclude that the absence of unified efforts, along with disparities in data and the lack of clear objectives for the restoration of free-flowing rivers, pose a significant constraint. It is essential to further acknowledge the necessity to address the opportunity costs, culturally important freshwater species, and climate change impacts. Collaborative solutions based on clear objectives are required to apply the ambitious goals of restoring free-flowing rivers in the context of the Nature Restoration Law.