The sensitivity of ionic liquids (ILs) to water affects their physical and chemical properties, even at relatively low concentrations, yet the structural thermodynamics of protic IL- (PIL-) water systems at low water concentrations still remains unclear. Using the rigorous Kirkwood-Buff theory of solutions, which can quantify the interactions between species in IL-water systems solely from thermodynamic data, we have shown the following: (1) Between analogous protic and aprotic ILs (AILs), the AIL cholinium bis(trifluoromethanesulfonyl)imide ([Ch][NTf2]) shows stronger interactions with water at low water concentrations, with the analogous PIL N,N-dimethylethanolammonium bis(trifluoromethanesulfonyl)imide ([DMEtA][NTf2]) having stronger water-ion interactions at higher water contents, despite water-ion interactions weakening with increasing water content in both systems. (2) Water has little effect on the average ion-ion interactions in both protic and aprotic ILs, aside from the AIL [Ch][NTf2], which shows a strengthening of ion-ion interactions with increasing water content. (3) Self-association of water in both PIL-water systems leading to the presence of large aggregates of water in IL-rich compositions has been inferred. Water-water interactions in [DMEtA][NTf2] were found to be similar to those of dialkylimidazolium AILs, whereas these interactions were much larger in the PIL N,N-dimethylethanolammonium propionate ([DMEtA][Pr]), attributed to the change in anion-water interactions.