We investigate the structural organization and microscopic dynamics of aqueous cholinium glycinate ([Ch]-[Gly]), a biocompatible ionic liquid (IL), by employing all-atom molecular dynamics simulations. Herein, we observe the effect of water content on the molecular-level arrangement of ions in the IL-water mixture through simulated X-ray scattering structure function, their partial components, and real-space correlation functions. The study reveals the presence of a principal peak in the total structure function of the neat [Ch][Gly] IL at around q = 1.4 angstrom(-1). The corresponding correlation tends to decrease and shifts toward shorter length scales with increase in the water content. It is found that the principal peak mainly originates from the correlations between counter ions. Hydrogen bond analysis reveals that water molecules compete with the anions to form hydrogen bond with the hydroxyl hydrogen of cation. Concomitantly, strong hydrogen bonding is also observed between [Gly](-) anion and water, which depreciates with the increasing hydration level. Hydrogen-bond autocorrelation function analysis manifests that average lifetimes of different possible hydrogen bonds decrease with increase in mole fraction of water. The mobilities of the ions are also significantly affected by water, showing a nonlinear increase with the increasing water content. The [Gly](-) anion is found to show faster dynamics on the addition of water as compared to [Ch](+) cation.