Partially saturated rock fracture flow informs on groundwater recharge processes, water affecting infrastructure, and water quality deterioration. This study examines partially saturated flow through natural fractures in double porosity media. Rock samples are characterised in terms of bulk mineralogical composition, as well as its geomechanical properties including, for instance, fracture aperture and roughness, representing the overall rock mass geometry. Samples are tested at different angles of inclination, being 0°, 23°, 60°, and 90° orientation. Samples are wetted while observing inflow and outflows from the dry to wetting and to the rewetting phase conditions; calculating water budgets, linear flow velocities, and Reynolds numbers. The change in the hydraulic head and the flow of water in the different cross-sectional areas follows the Bernoulli and continuity principle. The observed flow mechanism for shale is finger flow, and the flow regime is transitional turbulent flow at low flow meter discharge rates, and turbulent rotational flow for high flow meter rates. Conversely, the flow mechanism for quartzite is film flow, while the flow regime at high and low flow meter rates are turbulent and laminar rotational flow, respectively. These flow mechanisms show fluid instabilities and rapid infiltration of water under unsaturated continuous influx conditions. Preferential flow prevails in the fracture as water exits the fracture parallel or perpendicular to the flow direction. Subsequently, water may rewet the pre-existing flow paths from the initially dry phase, form new paths, merge flow paths, or the wetting front-width increases. Inclination affects the formation of the overall flow pattern in the fractures, but not the flow rate. The aperture of the shale is smaller than that of quartzite, and the width of the aperture influences the observed flow mechanisms, as tight discontinuities are more likely to have forces counteracting free water movement, affecting the permeability. Capillary forces are significant in narrower apertures, whereas gravitational forces are prominent in quartzite. Joint roughness coefficients show that the fracture surfaces are not identical; roughness induces turbulence and accounts for flow channelling.