Although species traits have the potential to disentangle long‐term effects of multiple, potentially confounded drivers in ecosystems, this issue has received very little attention in the literature. We aimed at filling this gap by assessing the relative effects of hydroclimatic and water quality factors on the trait composition of invertebrate assemblages over 30 years in the Middle Loire River (France). Using a priori predictions on the long‐term variation of trait‐based adaptations over the three decades, we evaluated the ability of invertebrate traits to indicate the effects of warming, discharge reduction and water quality improvement. Hydroclimatic and water quality factors contributed to up to 65% of the variation in trait composition. More than 70% of the initial trait response predictions made according to observed long‐term hydroclimatic changes were confirmed. They supported a general climate‐induced trend involving adapted resistance and resilience strategies. A partial confounding effect of water quality improvement acting on trophic processes was also highlighted, indicating that improved water quality management can significantly help to reduce some adverse effects of climate change. This trait‐based approach can have wider implications for investigating long‐term changes driven by multiple, potentially confounded factors, as frequently encountered in the context of global change.