The neat and aqueous solutions of the cholinium glycinate ionic liquid (IL), [Cho][Gly], at different water mole fractions, xws, are studied by molecular dynamics simulations. The changes in the local nanostructure of systems with composition have been determined by calculation of various structural distribution functions. Hydrogen bond (H-bond) attractions determine the major relative orientations of the oppositely and like charged nearest neighbors. The cation-anion H-bonds mainly form between the hydrogen of the hydroxyl or methyl groups of the cation and the carboxylate oxygen of the anion. A preferred (antiparallel) arrangement between adjacent [Cho]+ cations is due to the effective H-bond between the hydroxyl oxygen and the methyl hydrogen sites that promotes the like-charge cluster formation. Adding water decreases the occurrence probability of the [Cho]+···[Gly]-···[Cho]+ bridge structure in the aqueous solutions due to the formation of the [Gly]-···HOH···[Gly]- structure via H-bonding. Observed density trend versus xw is interpreted based on an interstice model and investigating the water cluster size distribution. Finally, the effect of xw on the infrared (IR) vibrational spectra were studied and blue and red shifts were observed for the stretching and bending vibrational modes of the hydroxyl group of [Cho]+, respectively. Current findings will improve the efficient engineering design and task-specific applications of aqueous solutions of bio-ILs consist of [Cho]+ and amino acid anions.