When investigating the fields of biogeography and macroecology, climate- and productivity-related variables are frequently identified as the strongest correlates of species-diversity patterns. These variables have been usually merged under the climate/productivity hypothesis and describe the direct and indirect actions of climate on species. Being among the most vulnerable ecosystems to climate change, streams and rivers are expected to be influenced both by climatic and trophic (i.e. productivity-related) factors. We propose here to distinguish the relative influence of the two processes on large-scale, long-term changes in the functional diversity of freshwater invertebrate communities over two decades in France. To this end, we designed two functional indices using invertebrate traits to surrogate the respective mechanisms: climate vulnerability and feeding specialisation. Using geographically weighted regression (GWR) models, we showed that trends in both indices, along with the initial regional species-pools, have significantly contributed to the overall long-term increase in functional diversity of invertebrate communities. In addition, we highlighted a strong geographical differentiation in the contribution patterns with the climate vulnerability effect decreasing with latitude and the feeding specialisation effect being higher in headwaters than in large rivers. Finally, taking into account this non-stationarity in the ecological processes and responses using GWR models allowed explaining about 75% of the long-term changes in the community diversity. Consequently, this study offers sound perspectives in predicting the future patterns of trends in functional diversity of communities under different scenarios of environmental changes, like climate and/or land-use.