Insufficient food during early life could limit the population growth of endangered Pallid Sturgeon Scaphirhynchus albus in the lower Missouri River. Shallow‐water habitat restoration is intended to provide nursery benefits, including food, for young sturgeon, but the effect of shallow‐water habitat on their diet is unknown. Age‐0 Pallid Sturgeon are rare, providing little opportunity for direct evaluation; however, studying the closely related and abundant Shovelnose Sturgeon S. platorynchus may provide valuable information to guide habitat restoration efforts. We compared diet, body condition (lipid content), and change in body weight (24‐h bioenergetics simulation) for postdrift, age‐0 sturgeon among five reaches ranging widely in shallow‐water habitat availability. Lipid content of satiated and emaciated laboratory‐reared individuals were compared with that of wild‐caught fish. In general, shallow‐water habitat availability appeared to have little effect on the variables examined. Regardless of reach, wild‐caught fish primarily consumed chironomids, and empty stomachs were rare. Additionally, differences in prey weight, lipid content, or the modeled change in body weight did not usually correspond to differences in shallow‐water habitat availability. Instead, we found annual differences, as prey weight consumed and the percentage of fish with modeled weight gain was often higher in 2015 than 2014, while the opposite was true for the percentage of fish with lipid content values that were comparable with the emaciated laboratory standard. Overall, our findings complement recent suggestions that shallow‐water habitat restoration efforts, as previously implemented, may not benefit sturgeon populations. Our results coupled with previous research suggest that the lower Missouri River prey base can support a stable Shovelnose Sturgeon population; however, additional research is needed to determine whether this applies to Pallid Sturgeon.