In this contribution, an insight into the interactions between ionic liquids (ILs), 1-butyl-3-methylimidazolium tetrafluoroborate, [Bmim]BF(4), and 1-allyl-3-methylimidazolium chloride, [Amim]Cl, and water is presented using near-infrared (NIR) spectroscopic measurements. Distinct differences were found in the NIR spectra of pure [Amim]Cl and [Bmim]BF(4), whereby we propose optimized conformations. It was found that the relative position of the anion with respect to imidazolium cation is different in these two ILs. The geometry difference determined their different interaction modes with water, for example, the NIR spectra in alkyl group region were different for these two ILs/H(2)O mixtures, irrespective of being in a water-rich region or IL-rich region. However, their NIR spectra for aromatic group were similar, whereby we deduced that for both ILs, the water molecules were favorable to form hydrogen bonds with the proton H2 on imidazolium ring, rather than H4 and H5. Furthermore, it was shown that water molecules preferred to interact with BF(4)(-), but Cl(-) interacted more specifically with aromatic C-H groups compared with BF(4)(-). This was confirmed by the fact that the supramolecular structure of aqueous [Bmim]BF(4) solution was destroyed as mole fraction of water surpasses 0.3979, which was lower than the value of 0.5822 for [Amim]Cl/H(2)O. These results would have important directive significance for the study of the aggregation behavior and recovery of hydrophilic ILs in water.