Few studies have addressed how the diversity of basal resources change with stream regulation and the potential consequences on river biota. We sampled invertebrates above and below a series of dams, over two years, at both downwelling and upwelling zones. In each zone, we recorded the daily temperature and flow variations, estimated the algal development, measured the available resources, and analysed carbon and nitrogen stable isotope compositions of the invertebrate community. The number of hydrological pulses were typically higher below the dams than above the dams especially during high-flow periods whereas the groundwater outlets had minor effects on invertebrate assemblages. Invertebrate abundance, richness and diversity tended to decrease below the dams. Co-inertia analysis showed that flow and temperature variations, and eutrophication explained most of the variance in the invertebrate assemblages, which comprised a higher number of resilient taxa below than above the dams. The proportions of pesticide-sensitive invertebrates were lower below the dams and ovoviviparous and more generalist taxa were prominent. We did not observe the expected CPOM decrease and FPOM increase downstream. Accordingly, the proportions of each functional feeding group were remarkably similar above and below the dams despite the long distance between the sectors (>100 kms). The diversity of basal resources used within assemblages progressively increased downstream above dams. In contrast, the diversity of resources used by organisms below the dams decreased from upstream to downstream suggesting a significant influence of flow regulation on aquatic food webs. Finally, the shorter trophic chains for the invertebrate assemblages below the dams suggests that the effects of stream regulation and eutrophication induced a simplification of food webs. To our knowledge, this study is the first to connect taxonomic and functional trait changes in response to multiple stressors with the associated modifications in isotopic niches within aquatic invertebrate assemblages. ContextUnderstanding how stream regulation and associated anthropogenic pressures act on aquatic assemblages and trophic niches is necessary to guide management actions. GoalWe aimed to investigate the functional responses (traits and trophic niches) of aquatic invertebrate assemblages to stream regulation and eutrophication. MethodsWe used univariate and multivariate analyses to compare the invertebrate assemblages above and below the dams and to assess the contributions of hydrology (including groundwater supplies to the river), temperature and eutrophication to the variability in the composition of invertebrate assemblages. We also considered the relative utilization of a selected set of traits describing invertebrate resilience, resistance and specialization to address the potential functional effects of stream regulation on invertebrate assemblages. Finally, carbon and nitrogen isotope analyses allowed us to characterize the length and width of invertebrate assemblage food webs as related to the availability and diversity of basal resources. ResultsInvertebrate abundance and richness generally decreased below the dams, with the highest impacts on insect taxa. Co-inertia analysis showed that stream regulation and eutrophication were main drivers of the aquatic invertebrate assemblages. The analysis separated the sites above and below the dams according to flow and temperature variation, whereas eutrophication appeared as a secondary stressor that separated the sites within each sector. Furthermore, the series of dams resulted in (i) a higher proportion of resilient (e.g., multivoltine) and resistant (ovoviviparous) taxa and a majority of generalists in assemblages below dams, (ii) an impact on the classical dynamics of CPOM (decrease) and FPOM (increase) sources from upstream to downstream, and (iii) a reduction in the diversity of resource use and in the trophic chain length of invertebrate assemblages below dams. The cooler and less oxygenated upwelling zones had lower invertebrate abundance; however, contrary to our expectation, the variation in the groundwater supply did not affect the composition of epigean invertebrate assemblages. ConclusionThis study provides insights about the impacts of flow regime alteration and eutrophication on food webs that may have been caused by regulation of permanent streams. To our knowledge, this is the first to connect taxonomic and functional trait changes in response to multiple stressors with the associated modifications in energy fluxes in aquatic invertebrate assemblages. This study suggests that bed stability, which is associated with a reduction in channel mobility below the dams and with moderate eutrophication, may provide the shelter and resources that can locally favour invertebrate assemblage dynamics and lessen the effects of flow regulation. In addition, the study suggests that the biological trait-based approach and isotope analysis are complementary approaches for addressing ecosystem functioning. The relative utilization of traits indicates the functional potential of aquatic invertebrate assemblages to face multiple stressors whereas isotope analysis is an expression of the actual effect of the stressors on the trophic structure of aquatic invertebrate assemblages.