The positive effects of water quality improvement on stream biodiversity in the temperate regions are expected to be at risk with the projected climatic changes. However, the processes and mechanisms behind the predicted threats remain uncertain. From long-term series of benthic invertebrate samples from temperate rivers and streams in France, we analyzed diversity and composition shifts over time in relation to geographic elements and human stressors. Mechanisms for community changes were investigated with a trait-based analysis for the entire dataset and for a selected caddisfly community module. We observed a 42% increase in the taxonomic richness of stream invertebrate communities over the last 25 years. A gradual trend induced by water quality improvement was distinguished from a more abrupt climate change-induced shift in communities around the year 2000. Trophic amplification – the intensification of trophic interactions and pathways through the food web – was identified as the mechanism behind the strong community shift. Four lines of evidence for this trophic amplification are highlighted: (i) higher dissolved oxygen concentrations indicated a shift in primary production, (ii) the trait-based analysis of entire communities showed a bottom-up food web amplification, (iii) the trait-based analysis of the community module evidenced feeding strategy shifts and increased food web interactions, and (iv) the abundance analysis of the community module showed a productivity increase. These results lend credit to persistent investments in water quality for improving stream biodiversity, and contrary to expectation, climate change impacts seem so far to have reinforced these positive effects.