Hyperfragmentation of rivers by anthropogenic barriers is a major threat to biodiversity. Restoration policies are being adopted worldwide to mitigate these impacts, particularly those on fish connectivity. We assessed the utility of a novel genetic index of fragmentation, the F INDEX , by monitoring real-time responses of two fish genera to restoration operations at 11 weirs in France. The F INDEX outperformed traditional genetic tools, detecting barriers more efficiently, and thereby improving estimates of recovery of connectivity following restoration. Most weirs had significant impacts on connectivity before restoration, especially the highest and steepest ones. Restoration actions systematically improved genetic connectivity, sometimes completely and in just a few months, with an overall halving of fragmentation levels. Our study demonstrates that current restoration policies are recovering genetic connectivity efficiently, and that practitioners may benefit from the F INDEX as a new operational tool to assess barrier strength for nonmigratory organisms and to plan and monitor riverine restoration.