MIL-101 is a chromium terephthalate-based mesoscopic metal-organic framework and one of the most porous materials reported to date. In this study, we investigate the adsorption of CO(2) and CH(4) in dehydrated and hydrated MIL-101 and the effect of terminal water molecules on adsorption. The atomistic structures of MIL-101 are constructed from experimental crystallographic data, energy minimization, and quantum mechanical optimization. The adsorption isotherm of CO(2) predicted from molecular simulation agrees well with experiment and is relatively insensitive to the method (Merz-Kollman or Mulliken) used to estimate the framework charges. Both the united-atom and five-site models of CH(4) predict the isotherm fairly well, though the former overestimates and the latter underestimates. Adsorption first occurs in the microporous supertetrahedra at low pressures and then in the mesoscopic cages with increasing pressure. In the dehydrated MIL-101, more adsorbate molecules are located near the exposed Cr(2) sites than the fluorine saturated Cr(1) sites. The terminal water molecules in the hydrated MIL-101 act as additional interaction sites and enhance adsorption at low pressures. This enhancement is more pronounced for CO(2) than for CH(4), because CO(2) is quadrapolar and interacts more strongly with the terminal water molecules. At high pressures, however, the reverse is observed, as the presence of terminal water molecules reduces free volume and adsorption. For the adsorption of CO(2)/CH(4) mixture, a higher selectivity is found in the hydrated MIL-101.