In the context of future evolutions of environmental conditions and human activities, predicting which species are likely to go extinct is perhaps one of the most fundamental yet challenging tasks for conservation biology. It is particularly true in freshwater ecosystems which tend to have the highest proportion of species threatened with extinction. In this context and based on a large data set provided by the French National Agency for Water and Aquatic Environment (598 sites sampled at least 8 consecutive years and distributed across France), we (1) quantified extinction and colonization rates for French river fish species at a local scale, (2) modelled independently the habitat suitability for fish species from local to large hydrological units and (3) tested if extinction/colonization rates for fish species could be predicted by the habitat suitability at various spatial scales. Results show that extinction and colonization rates depend on habitat suitability at local scale but also at the drainage basin scale. In terms of management, we show that habitat suitability quantification allows the evaluation of species extinction/colonization processes and our results reinforce the belief that the preservation of habitats at the local scale but also at the drainage basin scale enables the decrease of extinction risks of freshwater fish species.