In carbonates, fault zone architecture, distribution of different types of fault rocks in fault cores (e.g., breccias, cataclasites), and the interplay between deformation and diagenesis must be considered to predict the flow properties of a fault zone. We present the results of an integrated structural and petrophysical study of two carbonate outcrops in central Italy, where faults are known to act as dynamic seals at depth, causing ≈70 m of hydraulic head drop in a karstified groundwater reservoir. The architecture of these fault zones is very well exposed, allowing for detailed mapping of the along-strike and across-strike distribution and continuity of fault cores and associated fault rocks over a distance of ≈8 km. More than 150 samples, comprising several fault architectural elements and carbonate host rocks, were collected in transects orthogonal to the fault zones. Fault rock porosity and permeability were measured on 1-inch plugs and then linked to characteristic microstructures and fault rock textures. The results of this integration consisted of ranges of porosity and permeability for each type of fault rock. A trend of increasing comminution and decreasing pore size is evident from the outer toward the inner portions of fault cores. Three types of breccias (crackle, mosaic, and chaotic) and various types of cataclasites were identified. Crackle breccias show the highest plug permeabilities (up to hundredss of mD), whereas the ultracataclasites have the lowest plug permeability (down to 0.01 mD, which is roughly equivalent to unfractured host rock). These data reveal the interplay between various fault rocks and host rock permeability and the development of permeability anisotropy of fault zones in carbonates.