Fluid flow through a single fracture is traditionally described by the cubic law, which is derived from the Navier-Stokes equation for the flow of an incompressible fluid between two smooth-parallel plates. Thus, the permeability of a single fracture depends only on the so-called hydraulic aperture which differs from the mechanical aperture (separation between the two fracture wall surfaces). This difference is mainly related to the roughness of the fracture walls, which has been evaluated in previous works by including a friction factor in the permeability equation or directly deriving the hydraulic aperture. However, these methodologies may lack adequate precision to provide valid results. This work presents a complete protocol for fracture surface mapping, roughness evaluation, fracture modeling, fluid flow simulation, and permeability estimation of individual fracture (open or sheared joint/pressure solution seam). The methodology includes laboratory-based high-resolution structure from motion (SfM) photogrammetry of fracture surfaces, power spectral density (PSD) surface evaluation, synthetic fracture modeling, and fluid flow simulation using the Lattice-Boltzmann method. This work evaluates the respective controls on permeability exerted by the fracture displacement (perpendicular and parallel to the fracture walls), surface roughness, and surface pair mismatch. The results may contribute to defining a more accurate equation of hydraulic aperture and permeability of single fractures, which represents a pillar for the modeling and upscaling of the hydraulic properties of a geofluid reservoir.