Downstream of small-scale hydropower plants (SHPs), the intensity, frequency and persistence of hydropeaking events often cause an intolerable stress on fish of all life stages. Rapid increases in flow velocity result in fish avoiding unstable habitats and seeking refuge to reduce energy expenditure. To understand fish movements and the habitat use of native Iberian cyprinids in a high-gradient peaking river, 77 individuals were PIT tagged downstream of Bragado SHP in the North of Portugal. Tagged fish species included Pseudochondrostoma duriense and Squalius carolitertii. Fish positions were recorded manually on two different occasions: during hydropeaking events (HP) and without hydropeaking events (NHP). From the 77 tagged fish, we were able to record habitat use for 33 individuals (20 P. duriense and 13 S. carolitertii) in a total of 125 relocations. Fish species were distributed along the river reach with high density in the upstream area in the vicinity of the SHP tailrace, in particular during HP. Fish locations were associated with velocity for P. duriense and S. carolitertii. The latter tended to use faster flowing waters than P. duriense. Our findings on the habitat use in peaking rivers are a valuable tool to help in the selection and design of mitigation measures.