We evaluate, for the first time, variations of the national Fish-Based-Index (FBI) over a seventeen-year period for 1583 sampled sites evenly distributed across the French territory. As far as we know this is one of the first studies analyzing the temporal trends of a fish-based biotic indicator for such a consistent set of records going back over almost two decades. Our results provide four important insights. First, the index is efficient in discriminating sites in good condition from sites experiencing anthropogenic disturbances. Second, according to the index, the ecological state of French riverine fish assemblages is rather poor, as around half of the assessed sites, thought to reflect the diverse conditions within the French riverine system, are significantly impaired. Third, according to the index, there is no noticeable amelioration through time of sites fish assemblage structure and function despite management efforts initiated two decades ago to comply with the EU’s 2000 Water Framework Directive. Fourth, the index might start being influenced by climate change as early signs of response to warming are happening since the last 10 yr. According to the FBI, the current efforts for improving the biological condition of riverine systems in France are not yet creating desired outcomes.