Hydrated ionic liquids (ILs), including the choline-based amino acid ILs, [Ch][AA], with added inorganic salts are of particular interest because they have been found to be the best media for good solubility and structural stability of proteins. This contribution presents, for the first time, a study of the details of ion–solvent and ion-ion interactions in [Ch][AA]–water–NaCl (AA = Gly, Ala, Pro) systems, which mimic the proper environment for proteins. The local environment of ions in the systems under salt effect up to 2 M was analyzed withing the framework of RISM (Reference Interaction Site Model) theory in terms of radial and spatial distribution functions, as well as hydration numbers and possible associates. It was found that over the entire NaCl concentration range, the bioions of [Ch][AA] are well hydrated, revealing a strong ability to bind a significant amount of water. Moreover, at high NaCl concentrations in the mixture, there is a possibility for ion binding, with the [Ch]+-Cl– binding via the onium moiety by Coulomb interaction being a priority. Interestingly, the observed hydration and association features of bioions are similar to those exhibited by compatible osmolytes, which have a protective action on protein structure. The present data contribute new knowledge to our understanding of the interactions between ILs and their molecular environment, as well as their potential biological effects.