Recognizing how stream fish communities-and their habitats-differ across space and time relative to their position in stream networks (i.e., main-stem versus tributary habitats) is increasingly important for the conservation of imperiled native fish communities in altered river networks such as those in the Colorado River basin. We studied the patterns (community composition) and processes (movements) that shape species occurrences and distributions in two tributaries of the San Juan River, Utah and New Mexico, between 2012 and 2014. Our results show that distance from the San Juan River was a strong driver of tributary fish community structure, whether through declines in species richness (Chaco Wash) or species turnover (McElmo Creek), and that these patterns coincided with habitat gradients (i.e., depth, substrate, and width). Occurrences of passive integrated transponder (PIT)-tagged fish at a stationary antenna in McElmo Creek just upstream of its confluence with the San Juan River varied by species but generally were associated with spring spawning migrations (Flannelmouth Sucker Catostomus latipinnis, Razorback Sucker Xyrauchen texanus), exploratory movements (Colorado Pikeminnow Ptychocheilus lucius), and monsoon flooding (Channel Catfish Ictalurus punctatus, Razorback Sucker). Occurrences of PIT-tagged fish in Chaco Wash were dominated by endangered Razorback Suckers and Colorado Pikeminnows, suggesting that this habitat supplies useful habitat, forage, or both. Given the common occurrences of native fishes in these tributaries, incorporating these habitats into basinwide management actions seems necessary to fully understand the spatiotemporal dynamics of native and nonnative fish communities.