The molecular packing of amorphous maltodextrin-glycerol matrices is systematically explored by combining positron annihilation lifetime spectroscopy (PALS) with thermodynamic measurements and dilatometry. Maltodextrin-glycerol matrices are equilibrated at a range of water activities between 0 and 0.54 at T = 25°C to analyze the effect of both water and glycerol on the average molecular hole size and the specific volume of the matrices. In the glassy state, glycerol results in a systematic reduction of the average molecular hole size. In contrast, water interacts with the carbohydrate matrix in a complex way. Thermodynamic clustering theory shows that, at very low water contents the water molecules are well dispersed and are closely associated with the carbohydrate chains. In this regime water acts as an antiplasticizer, whereby it reduces the size of the molecular holes. Conversely, at higher water contents, while still in the glassy state, water acts as a plasticizer by increasing the average hole volume of the carbohydrate matrices. This plasticization-dominated mechanism is likely to be due to the interplay between the ability of water to form hydrogen bonds with the hydroxyl residues on the carbohydrate chains and its mobility, which is significantly decoupled from the bulk mobility of the matrix. Our findings are of key importance for the understanding of the effect of glycerol on the biostabilization performance of these carbohydrate matrices, as it provides a first insight on how molecular packing can relate to the dynamics in such matrices.