The hydration behavior of amino acids, essential for biological macromolecules, is influenced by ammonium biomaterials. The protic ionic liquids (PILs) are gaining attention in the food and pharmaceutical industries due to their nontoxicity and adjustable properties. Thus, study of the amino acids, such as L-proline, in the presence of PILs is crucial for understanding their hydration behavior. In this work, the effect of PILs, including mono, bis, tris (2-hydroxyethyl)ammonium acetate protic ionic liquids that might be naturally produced in human body, on L-proline hydration behavior was studied using COSMO calculations and thermophysical measurements. Measurements were the density, speed of sound, viscosity, and refractive index data of the solutions (L-proline + PILs + water) at various PIL concentrations at temperatures (298.15 to 318.15) K and under atmospheric pressure. The study indicates L-proline has weaker interactions with water compared to PILs ([2-HEA][Ac], [bis-2-HEA][Ac], and [tris-2-HEA][Ac]) due to its compact structure and lower negative dielectric energy. PILs interact more strongly with water through hydrogen bonding. Increasing temperature affects L-proline’s hydration layer, releasing more water molecules compared to PIL solutions. This effect is more pronounced with [tris-2-HEA][Ac], likely due to its larger size and complex structure. While L-proline promotes an ordered water structure, PILs can disrupt this by rearranging water molecules and forming their own hydrogen bonds.