Ionic liquids (ILs) have shown great potential in the dissolution and stability of biomolecules when a low-to-moderate quantity of water is added. Hence, determining the thermophysical properties and understanding these novel mixtures at the molecular level are of both fundamental and practical importance. In this context, here we report the synthesis of two nontoxic guanidinium cation based ILs, tetramethylguanidinium benzoate [TMG][BEN] and tetramethylguanidinium salicylate [TMG][SAL], and present a detailed comparison of their thermophysical properties in the presence of water. The results show that the [TMG][SAL]/water mixtures have higher density and higher apparent molar volume, but a lower viscosity and higher compressibility than the [TNG][BEN]/water mixtures. The measured viscosity and compressibility data are explained from ab initio quantum mechanical calculations and liquid-phase molecular dynamics simulations, where salicylate anions of denser [TMG][SAL]/water were found to exist as isolated ions due to intramolecular H-bonding. On the contrary, intermolecular H-bonding among the benzoate anions and their strong tendency to form an extended H-bonding network with water made [TMG][BEN]/water solutions more viscous and less compressible. This study shows the importance of probing these emerging solvents at the molecular-to-atomic level, which could be helpful in their optimal usage for task-specific applications.