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Changes in land use, climate and flow diversion are key drivers of river flow regime change that may eventually affect freshwater biodiversity and ecosystem functions. However, our knowledge is limited on how the functional features of stream organisms vary along the gradient of hydrological disturbance (i.e. flow regime changes) and how flow regimes mediate the functional features in lowland streams. We analyzed the functional traits of benthic diatoms (unicellular siliceous algae) that are most sensitive and tolerant to flow regime changes along a nationwide scale of 246 sites in Denmark. We combined RLQ and fourth-corner analyses to explore the co-variation between hydrological variables (R table) and species traits (Q table), constrained by the relative abundance of each species (L table) as observed in each of the sampling sites. Further, we examine the relationships between functional features (i.e., functional redundancy and diversity) and hydrological variables by multivariate statistical analyses. Results show that species turnover with displacement of sensitive species by tolerant species was the dominating process in benthic diatom communities during high flow disturbances. Functional features, as indicated by functional diversity and redundancy indices, were mediated mainly by high and low flow magnitude. Median daily flow magnitude shows a consistent positive relationship with functional redundancy and richness indices indicating that larger streams are more resilient to flow perturbations. In addition flow regime changes are less important than median daily flow magnitude and show inconsistent correlation to functional features likely due to the interaction of multiple environmental stressors. Our study highlights the robustness of trait-based approaches for identifying flow regime changes in streams, and strongly suggests that biodiversity conservation and water resource management should focus on protecting natural base flow in headwater streams and generally reduce flow regulation for sustaining stream ecosystems under future global changes. (c) 2018 Elsevier B.V. All rights reserved.