The impact of shear displacement under different mechanical boundary conditions on fluid flow and advective transport in a single fracture at the laboratory scale is demonstrated in the present study. The shear-induced changes of fracture aperture structures are determined by using the measured normal displacements and digitalized fracture surfaces from laboratory shear tests. Five shear tests on concrete replicas of the same fracture under different mechanical boundary conditions, including constant normal loading (CNL) and constant normal stiffness (CNS), are conducted to analyse the influence of mechanical boundary conditions on the shear-flow-transport processes. Fluid flow in the fracture with different shear displacements are simulated by solving the Reynolds equation. The Lagrangian particle tracking method is applied to model the advective transport in the fracture after shearing. The results generally show that the shear displacements and the normal loading conditions can significantly affect flow patterns and advective travel time distributions in the fracture. For mated fractures, the flow and transport will be enhanced by the increasing shear displacement because of shear dilation. For cases with the same shear displacement, the median advective travel time increases with the increasing boundary normal stiffness. The median advective travel time under the CNS boundary condition is generally longer than that under the CNL boundary condition. The results from this study can help to improve our understanding of stress-dependent solute transport processes in natural rock fractures. © 2021 The Author(s)