Cycles of low‐ and high‐water periods (i.e., years) in river systems are natural occurrences, but a clear understanding of how cyclical climatological patterns affect fishes, especially long‐lived species, is lacking. We compared Shovelnose Sturgeon Scaphirhynchus platorynchus population dynamics between a low‐water period (2001–2004) and a high‐water period (2009–2012) in the lower Platte River, Nebraska. Low‐flow periods in the lower Platte River can cause disconnections between upstream and downstream reaches, resulting in isolated pools and elevated water temperatures that create stressful situations for aquatic life and potentially lead to mortality. Our data showed no measurable differences in key population indices between flow condition periods, which is consistent with current paradigms for long‐lived fish species. Shovelnose Sturgeon relative weights were generally greater than 80 during both low‐ and high‐water periods, and size structure did not differ between the two periods. Shovelnose Sturgeon abundances, however, were significantly greater during high‐water conditions compared to low‐water conditions. Shovelnose Sturgeon may have migrated to more suitable habitats during low‐water periods to seek refuge, later returning after conditions improved. Shovelnose Sturgeon and other riverine fishes have evolved in a variable environment and have been able to endure relatively minor anthropogenic changes within the lower Platte River. Rivers like the lower Platte River that have retained much of their original physical features and flow regimes are likely key components for the resistance and resilience of riverine species. However, as alterations to landscapes continue, and given the uncertainty surrounding future climate predictions, it is unknown how these riverine species will be able to adapt to future changes. Reducing anthropogenic changes that disrupt flow regimes and increasing connectivity among river systems could provide greater amounts of refuge for fish during stressful conditions, thus helping to protect these riverine species.