The present work focuses on a numerical investigation of the flow through porous media with macropores, such as carbonates. The presence of vugs and fractures have a strong effect on the flow characteristics. The flow through the porous matrix is usually described by the Darcy equation and the flow through the macropores by Stokes equation. The coupling between these two distinct approaches brings great complexity to the modeling of such flows. In this work, we use Brinkman formulation that is able to describe the flow, both in the porous matrix and macropores with a single differential equation. We solved the set of differential equations using the finite element model and implemented the code in the FEniCS platform. We first solved the 1-D flow through parallel plates with one of the walls being a porous material. The goal was to compare the predictions obtained with the Brinkman formulation to that obtained by using the Beavers-Joseph boundary condition. Then, we solved a 2-D flow through a porous medium with macropores. The geometry of the pore structure was obtained from 2D slices of tomographic images of carbonates. The goal of this analysis was to evaluate an equivalent permeability as a function of macropores area and structures.