We report a systematic study to understand the structural dependence of protic ionic liquids, having ammonium or hydroxylammonium as cation and carboxylate as anion, on surface, optical, and transport properties. Experimental measurements of surface tension, refractive index, and electrical conductivity were investigated in the temperature range from (293.15 to 333.15) K at atmospheric pressure to understand the effect of the hydroxyl group on the cationic part and alky chain length and inclusion of highly electronegative fluorine atoms on the anionic part of studied protic ionic liquids. Further, surface entropy, surface energy, critical temperature, parachor, molar refraction, electronic polarizability, thermo-optic coefficient, and free volume were estimated from experimental values. Experimental electrical conductivity data were correlated using the Vogel-Tammann-Fulcher equation. The ionicity was assessed on the basis of the fractional Walden rule, and it was found that the studied protic ionic liquids fall below the ideal line. Upon hydroxyl group functionalization on the cationic chain length, the surface tension and refractive index of ionic liquids increase significantly, whereas the electrical conductivity decreases over the nonfunctionalized ionic liquid counterpart. Moreover, experimental and calculated results were explained to understand the effect of temperature and moiety of ionic liquid on studied thermophysical properties.