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We discuss techniques to represent groundwater flow in carbonate aquifers using the three existing modeling approaches: equivalent porous medium, conduit network, and discrete fracture network. Fractures in faulted stratigraphic successions are characterized by dominant sets of sub‐vertical joints. Grid rotation is recommended using the equivalent porous medium to match higher hydraulic conductivity with the dominant orientation of the joints. Modeling carbonate faults with throws greater than approximately 100 m is more challenging. Such faults are characterized by combined conduit‐barrier behavior. The barrier behavior can be modeled using the Horizontal Flow Barrier Package with a low‐permeability vertical barrier inserted to represent the impediment of horizontal flow in faults characterized by sharp drops of the piezometric surface. Cavities can occur parallel to the strike of normal faults generating channels for the groundwater. In this case, flow models need to account for turbulence using a conduit network approach. Channels need to be embedded in an equivalent porous medium due to cavities a few centimeters large, which are present in carbonate aquifers even in areas characterized by low hydraulic gradients. Discrete fracture network modeling enables representation of individual rock discontinuities in three dimensions. This approach is used in non‐heavily karstified aquifers at industrial sites and was recently combined with the equivalent porous medium to simulate diffusivity in the matrix. Following this review, we recommend that the future research combines three practiced modeling approaches: equivalent porous medium, discrete fracture network, and conduit network, in order to capture structural and flow aspects in the modeling of groundwater in carbonate rocks. [ABSTRACT FROM AUTHOR]