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Different types of Carbopols are frequently applied excipients of various dosage forms. Depending on the supramolecular structure, their water sorption behaviour could significantly differ. The purpose of the present study was to track the supramolecular changes of two types of Carbopol polymers (Carbopol 71G and Ultrez 10NF) alone and in their physical mixture with a water-soluble drug, vitamin B12, as a function of storage time. The combination of FT-IR spectroscopy, positron annihilation lifetime spectroscopy (PALS) and Doppler-broadening spectroscopy was applied to follow the effect of water uptake on the structural changes. Our results indicate that water-induced interactions between polymeric chains can be sensitively detected. This enables the prediction of stability of dosage forms in the course of storage.