In fluvial systems, the biological communities are mainly structured by the physical habitat. Knowing the habitat that each species use throughout its life is fundamental to understand its ecology in natural systems and to define conservation strategies in altered systems. For that reason, here we characterize the habitat use of 12 native fish species of the San Pedro River. 37344 individuals of the 13 native species occurring in the river were caught. Shallow ponds and shallow rapids were the most sampled habitats and had the largest captures. The most abundant species were Percilia gillissi, Galaxias maculatus, Galaxias. platei and Trichomycterus areolatus. A differentiated habitat use per species is notices, where the Galaxiids are more abundant in areas of slow velocity (ponds) and the Silurids in areas of high velocity (riffles). Moreover, we recognized a differentiated habitat use based on the size of Atherinopsidae and Percichthys trucha, where adults mainly occur in the lake and their juveniles occur in the borders of fluvial zones.