Understanding the fluid flow and solute transport in karst conduits is of great significance to the prevention of pollutants in karst areas and to reveal the mechanism of non-Fickian transport. Firstly, the evolution of eddies in semicircular rough conduits under different hydrodynamic conditions and their effects on solute transport were evaluated. Secondly, we find that the solute exchange between the main flow stream and the eddy zone is intensified with the gradual increase of the inlet flow velocity, weakening the non-Fickian effect. Finally, the transformation mechanism process of advection and hydrodynamic diffusion of solute into karst conduit was revealed. The relationship between the equilibrium concentration, corresponding time and flow velocity at different stages was quantified. This study can provide technical support for groundwater pollution control in karst area.