AbstractObjectiveCharacterizing habitat associations is useful to aid in understanding the habitat requirements of native fishes, particularly those of conservation concern. Our study objective was to characterize mesoscale habitat associations of the only remaining wild population of the Rio Grande Silvery Minnow Hybognathus amarus (a federally endangered desert river fish), and provide comparisons with mesohabitat availability in the middle Rio Grande, New Mexico, from 1994 to 1996.MethodsWe collected fish monthly at two sites (separated by 160 km) near the northern and southern limits of the species' current range, and we recorded depth, velocity, substrate, and mesohabitat type for each habitat surveyed. Mesohabitat availability was recorded across 10 equally spaced and fixed transect lines at both study sites.ResultRio Grande Silvery Minnow most frequently occupied mesohabitats characterized by relatively shallow depths (≤25 cm) and low to near‐zero water velocities (≤15 cm/s). Statistical analyses indicated that mesohabitats occupied by the species were not the most frequently available at the study sites, suggesting a preference for shallow, low‐velocity habitats. Relatively high abundance of Rio Grande Silvery Minnow (n = 10,971), especially compared with post‐2009 abundance, facilitated robust characterization of species‐specific habitat associations.ConclusionComparison of our results with other studies of pelagic broadcast‐spawning leuciscids (pelagophils) endemic to the Great Plains and desert rivers of North America suggested broad overlap in mesohabitat associations among members of this reproductive guild. Our work contributes to a growing body of research aimed at conserving this declining reproductive ecotype of freshwater fishes and suggests that increasing hydraulic diversity through innovative management approaches (e.g., habitat creation, restoration of fluvial processes, and preservation of natural streamflow characteristics) will be crucial for their long‐term recovery and conservation.