This work focuses on the spacing and height distributions of bed-perpendicular fracture sets present within a carbonate multilayer, and on their effect on the volumetric (P32 and fracture porosity) and hydraulic (correspondent permeability) properties of the rock mass computed after DFN modelling. Results of integrated field and laboratory analyses are consistent with an uneven spacing distribution of Strata-Bound (SB) fractures. The oldest SB fractures formed within individual limestone beds bounded by bed interfaces, which likely acted as mechanical interfaces. Differently, the youngest SB fractures formed within smaller rock volumes bounded by the pre-existing fractures. Non Strata-Bound (NSB) fractures consist on sheared bed-perpendicular fractures, originally compartmentalized within individual beds, which now form incipient strike-slip faults. DFN modelling of representative rock volumes show that both volumetric and hydraulic properties are strongly affected by the two main sets of NSB fractures, which form a conjugate system of faults producing the principal structural anisotropy in the fractured carbonate multi-layer.