Understanding the surface behavior of a porous natural stone in contact with a water source is of great importance for predicting the interaction of a certain material with the surrounding medium. Water in porous building materials plays a crucial role through the degradation process and affects some mineralogical and chemical compositions of the material. In this study, naturally hydrophilic surfaces of the porous intraclastic limestone and welded tuff were modified with a waterborne fluorinated polysiloxane agent and were made impermeable to water by dip coating process. Attenuated total reflectance Fourier transform infrared spectroscopy was used to verify the presence of the fluorinated siloxane compound on the surface. Contact angle and capillary water absorption analyses show that the hydrophobic character is due to the fluorinated carbon chain on the surface giving repellency to water as low-energy film-forming substance. Verifications of the color of untreated and treated stones were evaluated with colorimetric measurements. The changes in the contact angle and the capillary water absorption with simulated physical weathering conditions such as freezing-thawing and thermal shock cycles are also discussed. The research indicates the hydrophobic character and the initial colors of the selected stones were preserved up to a certain degree under extreme temperatures.