We investigate both laminar and turbulent flow regimes in a 3D rock fracture via numerical CFD simulations. We construct our realistic fracture model from 3D scan data of a fractured rock sample and implement changes in both shear displacement and contact ratio, examining their effect on fracture permeability and friction factor. While previous studies were investigating either fully viscous Darcy or inertial Forchheimer laminar flow regimes, we chose to cover the wide Reynolds number range of 0.1–\(10^6\). We introduce CFD simulation of a turbulent flow for realistic 3D fractures, implementing the RANS approach to turbulence modeling. We focus on 3D fracture geometries and implement changes in both shear displacement and contact ratio, systematically examining their effect on fracture permeability and friction factor in a manner similar to the fundamental studies of the flow in rough-walled pipes. Growing Re leads to first stationary–non-stationary and then laminar–turbulent transitions. The presence of contact spots severely disrupts the flow pattern and adversely affects the overall permeability of the fracture. Regardless of shear displacement, ‘no contact’ 3D models can be reasonably approximated by the 2D profiles. Depending on the fracture geometry, Forchheimer \(\beta\) fitting for both laminar and turbulent regimes can be performed either by a single or by two parameter values.