Abstract: | Interspecies and intraspecies variation in the use of wooded habitats has been studied for salmonids, but little is known about nonsalmonid species. In this study, we explored spatiotemporal differences in the distribution of three cyprinid species at habitats of varying wood density and at habitats of varying heterogeneity in a Mediterranean intermittent river (Evrotas, southern Greece). Hydroecological data from 843 microhabitats across four sites and in five sampling periods were collected and analysed using generalized linear mixed effects models. Adult chubs, minnowroaches, and minnows and, to a lesser degree, juvenile chubs, preferred complex, wooded habitats, characterized by lower flow velocities, higher water depths, finer substrate, and increased canopy cover, compared with wood‐free and noncomplex habitats. At the advanced stage of the dry period, the deeper, wooded habitats served as drought refugia; all fish groups, except for the adult chub, resorted to these habitats during autumn. In contrast, no such shifts were evident in early summer at the onset of the dry period. In late spring, all fish groups had higher densities at wooded habitats, a shift probably associated with reproduction. Wood density did not affect fish habitat use, as fish densities were similar across wooded habitats. In contrast, habitat heterogeneity significantly affected fish densities; more adult chubs and minnows were observed in complex habitats, whereas juvenile chubs and minnowroaches clearly preferred less complex habitats. We conclude that the targeted maintenance of instream wood structures to ensure habitat heterogeneity is a key‐action for the successful conservation of riverine fish populations. |