Abstract Microhabitat use by three endemic Iberian cyprinids, Barbus bocagei (Steindachner), Pseudochondrostoma polylepis (Steindachner), and Squalius pyrenaicus (Günther) was studied in terms of depth, mean water column velocity, focal height, focal velocity, distance to shore and substrate. Data were obtained by snorkelling during spring and summer at nine sites of the Tagus River Basin, Spain. Habitat suitability criteria (HSC) were calculated, including fish position and focal velocity in the water column. Species comparison showed differences in depth and focal height (indicating a vertical segregation), and greater water velocities for Pseudochondrostoma. Size-class comparisons mainly showed differences in depth and focal height (correlated with fish size). The fish groups (3 species × 3 length classes) were assigned to microhabitat functional types. The results are essential for environmental flow assessments and allow 2- and 3-dimensional habitat simulations in Mediterranean rivers; they are also useful to define critical habitats for the conservation of native fish populations.