Modeling of coupled hydro-mechanical and chemical (HMC) processes in fractured rocks is an important topic for many geoengineering projects.  Over the past decades, many efforts have been devoted to study the flow and transport in single fractures with consideration of mechanical effects. It is generally known that the mechanical effects, i.e. normal and shear deformation, significantly affect fluid flow and solute transport processes in rough-walled rock fractures since the deformation may largely alter the structure of fracture apertures that directly controls transmissivity. Due to complicated physical processes combined with complexity of geometry structures, many issues remain open questions, such as fracture surface roughness characterization, deformation dependence of transmissivity and advective transport in natural rock fractures. In this work, we attempt to investigate the impact of stress caused closure on fluid flow and solute advective transport in a rough-walled fracture through numerical modeling.  A rough-walled fracture model is created based on a laser-scanned rock surface. The Bandis’s model is used to describe the fracture closure subject to normal stress. The flow is modeled by solving Reynolds equation and the advective transport is simulated through Lagrangian particle tracking. The results show that the normal stress caused fracture closure creates asperity contacts and reduces the mean aperture, which significantly reduces transmissivity, and affects the travel time and transport resistance. With increases of normal stress, the specific surface area reduces nonlinearly due to the nonlinear closure. In practice, especially for important hydrogeological projects, e.g. nuclear waste disposal, it is important to consider the coupled HMC processes in design and risk assessment.