Water changes the physical properties of ionic liquids (ILs). In this paper, the effect of water on ILs is investigated at the molecular level. The molecular structure and arrangement of 1-butyronitrile-3-methylimidazolium halide, in the presence and absence of the intruded water molecule, have been elucidated by single-crystal X-ray crystallography and near-infrared Raman spectroscopy. Water molecule is found to change the conformation of the n-butyronitrile chain of the cation. The hydrogen bonding interaction between the anion and water molecule, leading to loose molecular packing, is most likely to be responsible for the change. Distinct molecular structures and arrangements of ILs with and without water molecule have been presented here for the first time. As the unique properties of ILs are related to their structures and molecular arrangements, the presence of water, wanted or unwanted, must be carefully examined in any kind of IL research and applications.