The degradation of aquatic ecosystems, induced by worldwide intensification in the use of both land and aquatic resources, has highlighted the critical need for innovative methods allowing an objective quantification and rank- ing of anthropogenic pressure effects on aquatic organisms. Such diagnostic tools have a great potential for defin- ing robust management responses to anthropogenic pressures. Our objective was to explore how the outputs of three diagnostic tools (based on benthic diatoms, macroinvertebrates and fishes) could be combined to (i) disentangle the temporal effects of multiple pressures over two decades and (ii) provide policy-relevant information for stream managers and decision makers. The diagnostic tools estimated, using taxonomy- and trait-based metrics, the impairment probabilities of biotic assemblages over time by different pressure categories, describing the alteration of water quality, hydromorphology and land use related to anthropogenic activities, in French streams (number of sites = 312). The main result shows that a large proportion of the time series exhib- ited no significant temporal patterns over the two decades (61.5% to 87.8%, depending on the used tests). Among time series exhibiting significant change, positive trends in impairment probabilities (i.e., degradation) were less frequent than negative ones, indicating a modest improvement in water quality at national scale over the study period. However, trends can be substantially different according to hydroecoregion and pressure category. The three biological compartments displayed convergent temporal responses according to the pressure category and regional context (e.g., lowland plains vs. mountains, pristine vs. agricultural regions). Altogether, this study proposes a unifying approach to integrate a vast amount of information in a single ecological diagnosis using an unparalleled database on natural and anthropized environments. Strengthening the synthesis of biological infor- mation provided by various biological compartments should be a priority before implementing evidence-based sustainable conservation and restoration actions.