The hydraulic conductivity of rock joints is an important parameter controlling fluid flow in various rock engineering applications. The shearing and normal loading have significant effects on hydraulic conductivity of rock joints, the property of which is mainly controlled by hydraulic aperture. Despite the importance of hydro-mechanical behaviour of rock joints, the fundamental micro-scale processes leading to macro-scale observations remain unexplored partly due to difficulties with in situ measurement of hydraulic aperture and its complex relation to roughness and contact area. Therefore, in this study, a series of experiments coupling fluid flow with normal deformability and direct shear are performed on joints with varying controlled roughness at different normal stresses. Along with measuring stress and flow rate, the time-lapse X-ray micro-computed tomography is carried out to explore the evolution of joint aperture and contact area during the experiments. The results of the normal deformability experiments show that the joint conductivity is well correlated to the mean hydraulic aperture of joint profiles. Such correlation, however, is not apparent for the shearing experiment where under high normal stresses, the flow rate decreases continually indicating that damaged asperities hinder the fluid flow. Despite the trend in the average mechanical aperture not following the flow rate in some cases, the trend in the contact area follows the flow rate very closely throughout the shearing process. In addition, the results reveal that despite an increase in contact area with increase in normal stress, it is not physically possible to reach full contact even for the artificially well-mated samples at a high normal stress of 10 MPa. Finally, a new correlation is proposed to relate the hydraulic aperture to joint average mechanical aperture, contact area and roughness. The correlation estimates the experimental flow rates at both normal and shear loading conditions with good accuracy.