A comprehensive model to describe the water stability of prototypical metal–organic frameworks (MOFs) is derived by combining different types of theoretical and experimental approaches. The results provide an insight into the early stages of water-triggered destabilization of MOFs and allow detailed pathways to be proposed for the degradation of different MOFs under aqueous conditions. The essential elements of the approach are computing the pKa values of coordinated water molecules and geometry relaxations. Variable-temperature and pH infrared spectroscopy techniques are used to corroborate the main findings. The model developed herein helps to explain stability limits observed for several prototypical MOFs, including MOF-5, HKUST-1, UiO-66, and MIL-101-Cr, in aqueous solutions, and thus, provides an insight into the possible degradation pathways in acidic and basic environments. The formation of a metal hydroxide through the autoprotolysis of metal-coordinated water molecules and the strength of carboxylate–metal interactions are suggested to be two key players that govern stability in basic and acidic media, respectively. The methodology presented herein can effectively guide future efforts, which are especially significant for in silico screening, for developing novel MOFs with enhanced aqueous stability.