Habitat use of eight native fish species was determined by electroshocking depth‐stratified lanes < 0.125 m, 0.125–0.25 m, 0.25–0.5 m, and 0.5–0.75 m. Two runs and two riffles were sampled in 34 rivers. Water depth, velocity, and substrate size were measured. Bluegilled bullies (Gobiomorphus hubbsi), upland bullies (G. breviceps), common bullies (G. cotidianus), longfinned eels (Anguilla dieffenbachii), and shortfinned eels (A.australis) made up over 80% of the total number and biomass of fish sampled. Overall, fish densities were highest along river margins in depths of less than 0.25 m, and higher in riffles than in runs. The fish species could be classified into four habitat guilds: a fast‐water guild that occupied central portions of riffles, an edge‐dwelling guild, an intermediate guild, and finally a guild that was ubiquitous. Minimum flow requirements based on habitat for the edge‐dwelling and fast‐water guilds would be conflicting, with one benefiting from low flows and the other from high flows. A minimum flow assessment based on the intermediate guild provides a compromise between these two extremes.