We use density functional theory meta-GGA TPSS+D3(BJ)+U+J calculations to investigate the energetics and geometry of water molecules in the flexible metal-organic framework material MIL-53(Cr) as a function of cell volume. The critical concentration of water to cause the transition from the large pore (lp) to the narrow pore (np) structure is estimated to be about 0.13 water molecule per Cr. At a concentration x = 1 water molecule per Cr, the zero-temperature np and lp configurations each have a hydrogen bond between the H of each framework hydroxyl group and a water oxygen (O W ). At intermediate volumes, water dimer-like configurations are observed. A concentration x = 1.25 leads to hydrogen bonding between water molecules in the np phase that is absent for x = 1. Our results suggest possible mechanisms for pore closing in hydrated MIL-53(Cr).