Natural stones are used as coating material on the exteriors and terraces of buildings in architecture, and in places such as entrances, halls, living rooms, kitchens, bathrooms and stairs in interior spaces. Limra limestone and travertine are used as natural building materials in many structures depending on their colors. However, the water absorption values of these two natural stones are high due to their porosity, resulting in negative effects from atmospheric conditions. In this study, two different carbonate-based natural stones, limra limestone and travertine, were treated with two different water-repellent chemicals, one solvent-based and one water-based. After application, thermal shock tests were performed with a sodium chloride solution consisting of twenty cycles. The changes in the weights of samples dried to constant mass, ultrasonic permeability, Leeb hardness, and color change values in the samples were determined after the thermal shock tests. In addition, the effects of water-repellent chemicals on the formation of NaCl crystals accumulated in the pores of the rocks were examined by SEM and EDX analysis. Changes in non-destructively measured values were compared with the values of reference samples without surface protection. The solvent- based water-repellent chemical made the sample surface more hydrophobic than the water-based repellent. In both types of natural stones, the solvent-based water repellent chemical showed more protective properties against salt crystallization under thermal shock conditions compared to the water-based repellent.