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We have studied the properties of water adsorbed inside nanotubes of hydrophilic imogolite, an aluminium silicate clay mineral, by means of molecular simulations. We used a classical force field to describe the water and the flexible imogolite nanotube, and validated it against data obtained from first-principles molecular dynamics. With it, we observe a strong structuration of the water confined in the nanotube, with specific adsorption sites and a distribution of hydrogen bond patterns. The combination of number of adsorption sites, their geometry and the preferential tetrahedral hydrogen bonding pattern of water leads to frustration and disorder. We further characterize the dynamics of the water, as well as the hydrogen bonds formed between water molecules and the nanotube, which are found to be more than one order of magnitude longer than water–water hydrogen bonds.