A significant amount of the base flow of the Santa Ana River, located within California's arid Los Angeles metropolitan region, originates from two wastewater treatment facilities: the Rialto wastewater treatment facility and Rapid Infiltration and Extraction facility. The Santa Ana sucker (Pantosteus santaanae, syn. Catostomus santaanae) and arroyo chub (Gila orcuttii) are two native species listed in the Upper Santa Ana Habitat Conservation Plan, which aims to balance water supply needs with the ecological needs of native fauna. Consequently, an understanding of the habitat needs of these fishes will play a crucial role in achieving the goals outlined by the conservation plan. We used fish presence during snorkel surveys with habitat availability surveys to quantify habitat selection by both native fish species within a resource selection function analytical framework. We found that both species selected habitat near structures that could serve as refugia from potential predators. In addition, Santa Ana sucker selected habitats with high gravel and cobble substrate composition, presumably to fulfill complementary habitat needs such as foraging and spawning. Our results suggest that habitat alterations due to water management infrastructure and an increasing population size of nonnative predators may also affect native fish habitat selection in the Santa Ana River.