Hydration of cross-linked starch microspheres, commercially available as a medical device, was investigated using a multi-method approach. We found that the uptake of water is accompanied by substantial swelling and changes of the polymer structure. Sorption calorimetry provided information about thermodynamics of water sorption, revealed presence of isothermal glass transition and absence of hydration-induced crystallization, observed in non-cross linked starch material. The changes in the surface and bulk properties of microspheres at different water–starch concentrations were investigated using synchrotron radiation X-ray scattering and analyzed using concept of fractals. The obtained information, combined with the results of differential scanning calorimetry, was used to construct a phase diagram of the studied material. Finally, hydration induced evolution of polymer structure revealed by the X-ray scattering was linked to the changes observed during swelling with optical microscopy.