In this paper, we investigate flow with solute transport in fractured porous media. The system of the governing equations consists of the continuity equation, Darcy’s law, and concentration equation. A discrete-fracture model (DFM) has been developed to describe the problem under consideration. The multiscale time-splitting method was used to handle different sizes of time-step for different physics, such as pressure and concentration. Some numerical examples are presented to show the efficiency of the multi-scale time-splitting approach.