Rock permeability, an important factor in subsurface fluid migration, can be influenced by microcracks and chemical weathering due to water–rock interactions. Understanding the relationship between permeability, chemical weathering, and microcracks is crucial for assessing fluid flow in rocks. This study focuses on the hydrogeological characteristics of granite and gneiss, potential host rocks for high-level radioactive waste disposal in South Korea. Samples were analyzed for permeability, porosity, P-wave velocity, and chemical weathering indices. Regression analysis revealed a weak correlation between permeability and both porosity and rock density, while an inverse correlation was observed between permeability and chemical weathering indices. Interestingly, some samples showed low permeability (10−21 to 10−22 m2) despite high weathering, while others showed high permeability (10−18 to 10−19 m2) despite low weathering. SEM-EDS analysis indicated the presence of microcracks within the rocks or the filling of these cracks with secondary minerals. The findings suggest that chemical weathering generally increases pore size and porosity, but actual permeability can vary depending on the presence and connectivity of microcracks and the extent to which they are filled with secondary minerals. Therefore, both chemical weathering and microcrack connectivity must be considered when evaluating the hydrogeological characteristics of crystalline rocks.