Otoliths, calcium carbonate (CaCO3) ear bones, are among the most commonly used age and growth structures of fishes. Most fish otoliths are comprised of the most dense CaCO3 polymorph, aragonite. Sturgeon otoliths, in contrast, have been characterized as the rare and structurally enigmatic polymorph, vaterite—a metastable polymorph of CaCO3. Vaterite is an important material ranging from biomedical to personal care applications although its crystal structure is highly debated. We characterized the structure of Lake Sturgeon otoliths using thermal analysis and neutron powder diffraction, which is used non-destructively. We confirmed that while Lake Sturgeon otoliths are primarily composed of vaterite, they also contain the denser CaCO3 polymorph, calcite. For the vaterite fraction, neutron diffraction data provide enhanced discrimination of the carbonate group compared to x-ray diffraction data, owing to the different relative neutron scattering lengths, and thus offer the opportunity to uniquely test the more than one dozen crystal structural models that have been proposed for vaterite. Of those, space group P6522 model, a=7.1443(4)Å, c=25.350(4)Å, V=1121.5(2) Å3 provides the best fit to the neutron powder diffraction data, and allows for a structure refinement using rigid carbonate groups.