The extent of fish movements in contemporary river networks can depend on spatial position relative to attractive features that may provide food and refuge, such as tributary mouths, or restrictive features, such as barriers. From the San Juan River basin in New Mexico and Utah, we integrated remote summertime PIT tag detections at two tributary mouths (McElmo Creek and Chaco Wash) with main‐stem recapture data from 2012 to 2015 to determine if two endangered species, Colorado Pikeminnow Ptychocheilus lucius and Razorback Sucker Xyrauchen texanus, differed in tributary use, demography, and seasonal ranges. Razorback Suckers were more abundantly detected (n = 266 individuals) and recaptured (n = 145) than were Colorado Pikeminnows (n = 96 detected; n = 55 recaptured). Despite the San Juan River flowing uninterrupted between the tributary mouths, individuals of each species separated into tributary‐specific groups. Razorback Suckers had very similar sizes and ages at each tributary, reflecting a homogeneous augmented population. Colorado Pikeminnows separated into tributary‐specific groups of either adult (Chaco Wash) or subadult (McElmo Creek) fish based on total length and age. Analyses suggested that fish size was a significant factor explaining the extent of seasonal ranges for both species. Although the ranges of both species exhibited a tributary effect, this effect was more significant in explaining Razorback Sucker ranges than Colorado Pikeminnow ranges, which were explained best by season. Understanding how mobile species interact with attractive and inhibitive river features can help managers identify potential sampling biases along with possible consequences of spatially structured populations. Managers should consider extending sampling upstream of barriers, installing additional permanent antenna arrays, and maintaining perennial flows in these tributaries.