Freezing hydrogels can compromise their network structures and modify their properties as a result of ice crystal formation. Therefore, understanding the internal structure, including ice crystals and the state of chemical components within hydrogels, is essential. In this study, we evaluated the elemental distribution in bio-based hydrogels subjected to freezing-thaw process using X-ray absorption spectroscopy with synchrotron radiation. A bio-based hydrogel, prepared from Alaska pollock, underwent both slow and rapid freezing processes. Tomographic images and linear X-ray absorption coefficient distributions of the rapidly frozen hydrogel displayed a uniform image with a mean absorption coefficient of 2.81 cm−1. Conversely, the slowly frozen sample exhibited distinct contrasts with peaks at 2.516 cm−1 (dark) and 3.691 cm−1 (bright), occupying 28% and 72% of the image, respectively. The mean absorption coefficient of the slowly frozen sample was comparable to that of the rapidly frozen sample, indicating no elemental loss. The elements within the hydrogel were categorized into organic elements, macrominerals, and trace elements. The bright areas in the images were attributed to the concentration of macrominerals. Notably, Cl and Na were the primary contributors to the absorption coefficients among the elements present, signifying salt migration during freezing. These findings suggest that the contrast observed in X-ray computed tomography images after freezing reflects the elemental distribution within the hydrogel and successfully demonstrates element localization due to cryoconcentration.