The reference condition approach, advocated by the Water Framework Directive, is the basis of most currently used multimetric indices using functional traits of fish species. The ecological status of streams is assessed by measuring the deviation of the observed trait values from the theoretical values of reference conditions in the absence of anthropogenic disturbances. While reference conditions serve as baselines for ecological assessment, they vary with natural environmental conditions. Therefore, global warming appears to be a major threat to the use of current indices for diagnosing future stream conditions, as climate change is projected to modify assemblage composition, suggesting that the functional structure of fish assemblages will also be affected. The main objectives of this study are to assess the potential effect of climate change on the trait composition of fish assemblages and the consequences for the establishment of reference conditions. The results highlight the relation between environmental, especially climatic, conditions and functional traits and project the effects of climate change on trait composition. Traits based on species intolerance are expected to be most negatively affected by the projected climatic shift. The consequences for the development of multimetric indices based on fish functional traits are discussed.