Monitoring the hydraulic properties within subsurface fractures is vitally important in the contexts of geoengineering developments and seismicity. Geophysical observations are promising tools for remote determination of subsurface hydraulic properties; however, quantitative interpretations are hampered by the paucity of relevant geophysical data for fractured rock masses. This study explores simultaneous changes in hydraulic and geophysical properties of natural rock fractures with increasing normal stress and correlates these property changes through coupling experiments and digital fracture simulations. Our lattice Boltzmann simulation reveals transitions in three-dimensional flow paths, and finite-element modeling enables us to investigate the corresponding evolution of geophysical properties. We show that electrical resistivity is linked with permeability and flow area regardless of fracture roughness, whereas elastic wave velocity is roughness-dependent. This discrepancy arises from the different sensitivities of these quantities to microstructure: velocity is sensitive to the spatial distribution of asperity contacts, whereas permeability and resistivity are insensitive to contact distribution, but instead are controlled by fluid connectivity. We also are able to categorize fracture flow patterns as aperture-dependent, aperture-independent, or disconnected flows, with transitions at specific stress levels. Elastic wave velocity offers potential for detecting the transition between aperture-dependent flow and aperture-independent flow, and resistivity is sensitive to the state of connection of the fracture flow. The hydraulic-electrical-elastic relationships reported here may be beneficial for improving geophysical interpretations and may find applications in studies of seismogenic zones and geothermal reservoirs.