Microcomputed tomography (μCT) and Lattice Boltzmann Method (LBM) simulations were applied to continental carbonates to quantify fluid flow. Fluid flow characteristics in these complex carbonates with multiscale pore networks are unique and the applied method allows studying their heterogeneity and anisotropy. 3D pore network models were introduced to single-phase flow simulations in Palabos, a software tool for particle-based modelling of classic computational fluid dynamics. In addition, permeability simulations were also performed on rock models generated with multiple-point geostatistics (MPS). This allowed assessing the applicability of MPS in upscaling high-resolution porosity patterns into large rock models that exceed the volume limitations of the μCT. Porosity and tortuosity control fluid flow in these porous media. Micro- and mesopores influence flow properties at larger scales in continental carbonates. Upscaling with MPS is therefore necessary to overcome volume-resolution problems of CT scanning equipment. The presented LBM-MPS workflow is applicable to other lithologies, comprising different pore types, shapes, and pore networks altogether. The lack of straightforward porosity-permeability relationships in complex carbonates highlights the necessity for a 3D approach. 3D fluid flow studies provide the best understanding of flow through porous media, which is of crucial importance in reservoir modelling.