The ability of young fish to find and consume food during early life history is an important factor affecting survival and recruitment. While dietary assessments for age-0 Scaphirhynchus sturgeon (shovelnose sturgeon and pallid sturgeon) in the Missouri River, USA have received increased attention over the last 15 years, there is currently limited information available to evaluate long-term trends in prey consumption and body condition. To better understand interannual factors during early-life history, we examined foraging and body condition of age-0 (<12.0 cm) Scaphirhynchus in relation to discharge and the availability of hypothesized foraging and food-producing habitats at a single reach (Lexington) of the Missouri River over a span of five years (2014–2018). Relatively high discharge in 2015 led to concomitant maxima in foraging and lipid levels for age-0 sturgeon. However, lower water levels in 2014 did not see declines in lipid content as would be expected given the low level of foraging observed that year. Additionally, the availability of hypothesized foraging and food-producing habitats had little effect on age-0 sturgeon prey consumption and condition in the Lexington Reach. Our results suggest that other factors in addition to river discharge may affect age-0 sturgeon foraging and condition and more research focused on understanding the flow-habitat relationships would be critical.