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The importance of flow‐related factors to benthic organisms, as well as the role of habitat conditions in shaping aquatic communities during low‐flow periods, have been recognised. Despite this, the preferences of macroinvertebrates to the ratio of lentic to lotic habitats at the reach scale have not been accurately quantified in most instances.Aquatic invertebrates and habitat features in a range of temporary rivers in Sardinia were investigated. The investigation focused on the flow‐related characteristics that contribute to defining the lentic–lotic condition of the river reaches. The relation of habitat features to benthic taxa distributions was assessed using multidimensional scaling. The main aim of the paper was to quantify the responses of taxa to the different lentic and lotic habitat conditions by applying hierarchical logistic regressions. Finally, taxon optima were aligned along the lentic–lotic gradient and the responses of different taxonomic groups compared.Unbroken waves and imperceptible flow were correlated with benthic taxa variability, suggesting local hydraulics and turbulence have a major role in regulating community composition. The overall lentic–lotic character of the river reaches was also clearly related to the benthic taxa distribution. More than 80% of taxa were significantly related to the lentic–lotic gradient, and an asymmetrical response curve was the predominant model.Benthic groups showed taxon optima clustered in different ranges of the lentic–lotic gradient. Odonata, Coleoptera, Hemiptera, and Mollusca preferred clearly lentic conditions. Diptera mainly ranged on the lotic side of the gradient, while Trichoptera were relatively uniformly distributed across the gradient. Ephemeroptera taxa clustered in intermediate lentic–lotic conditions, with two species preferring extremely lentic habitats. In general, optima converged at intermediate and extremely lentic conditions, presumably due, respectively, to the coexistence of different lentic and lotic features and to the highly diverse environmental characteristics under extremely lentic situations.These results support the conclusion that dissimilar ecological factors act on benthic taxa along the lentic–lotic range and species favouring different lentic–lotic conditions are subjected to pressures of different nature. This should not be ignored when defining species preferences and studying community structure or relationships between species in Mediterranean rivers, which cyclically vary their habitat composition. In addition, the uneven distribution of optima of different groups along the lentic–lotic gradient might affect macroinvertebrate metrics when assessing ecological status or establishing reference conditions under variable climatic conditions. [ABSTRACT FROM AUTHOR]