Alteration of flow regimes by anthropogenic activities is one of the primary environmental problems in riverine systems. Understanding how hydrologic conditions can affect ontogenetic habitat shifts of imperiled fishes is important in order to develop conservation and management strategies for each life-history stage. We examined relationships between the abundance of young-of-the-year (YOY) Rio Grande Blue Sucker and various abiotic variables in the Trans-Pecos region of the Rio Grande in Texas, USA. We used open N-mixture modeling to better understand the factors affecting ontogenetic habitat shifts of the imperiled aridland river fish. In addition, we examined differences in Rio Grande Blue Sucker total length among three mesohabitat types (pool, riffle, and run). The results of open N-mixture modeling suggested that as pool area increased, the abundance of YOY Rio Grande Blue Sucker increased. Total length of YOY Rio Grande Blue Sucker also significantly differed among the three mesohabitat types. The total lengths of YOY Rio Grande Blue Sucker in pool habitats were lower than in other mesohabitats, suggesting that YOY Rio Grande Blue Sucker undergo ontogenetic habitat shifts into greater current velocity habitats as they grow. The habitat associations we documented support the growing body of research emphasizing the importance of maintaining sufficient and appropriately timed flows to avoid prolonged low flows that limit habitat availability for native fish species during sensitive life stages in the Rio Grande and other aridland rivers.