Sicklefin (Macrhybopsis meeki) and sturgeon chub (M. gelida) historically occurred throughout the Missouri River (MR), in some tributaries, and Mississippi River downstream of the MR. They have been species of U.S. state-level conservation concern and U.S. Endangered Species Act listing candidates since the 1990s. We applied analytical approaches from occupancy modeling to correlation to monitoring data spanning 23 years to assess relationships between occupancy and time, space, environmental factors, habitat, and other species. Sicklefin chub occupancy appeared higher in the early to mid-2000s and mid-to-late 2010s. A potential decline in occupancy occurred for sturgeon chub in the mid-to-late 2010s. Spatially, chub occupancy was depressed for 159 to 438 km downstream of MR dams. Among macrohabitats, inside bends had relatively high occupancy for both species; secondary connected channels had relatively high values for sturgeon chub. Co-occurrence was likely between sicklefin and sturgeon chub and between chubs and shovelnose sturgeon (Scaphirhybchus platorybchus) and channel catfish (Ictalurus punctatus). The observed co-occurrence of chubs and pallid sturgeon (Scaphirhynchus albus; PS) was potentially higher than expected for adult PS. For juvenile PS, co-occurrence was lower than expected in the Lower MR and potentially higher than expected in the Upper MR, warranting future research. Results from this research suggest management for the improvement of sicklefin and sturgeon chub populations may benefit other MR fish populations.