Sorption of water by glassy biopolymers and the effects of absorbed water on molecular mobility including plasticization, matrix rearrangements, and diffusion are poorly understood mainly because molecular and structural analyses are scarce. Here, we report the first investigation of the nanostructure of amorphous carbohydrates and the plasticizing effects of water by combining positron annihilation lifetime spectroscopy (PALS) and thermodynamic analysis. Surprisingly, we find that the average volume of the voids between the polymer chains increases with the water content of the matrix while the density of the matrix increases. Consequently, the free volume of the carbohydrate matrix decreases continuously up to the glass transition, primarily by the filling or elimination of the smallest intermolecular voids. We conclude that a so far unknown length scale, the typical size of intermolecular voids, is of fundamental importance in understanding the interaction of water with amorphous carbohydrates and their ensuing plasticization.