A parallel implementation of an immersed-boundary (IB) method is presented for low Reynolds number flow simulations in a representative elementary volume (REV) of porous media that are composed of a periodic array of regularly arranged structures. The material of the structure in the REV can be solid (impermeable) or microporous (permeable). Flows both outside and inside the microporous media are computed simultaneously by using an IB method to solve a combination of the Navier–Stokes equation (outside the microporous medium) and the Zwikker–Kosten equation (inside the microporous medium). The numerical simulation is firstly validated using flow through the REVs of impermeable structures, including square rods, circular rods, cubes, and spheres. The resultant pressure gradient over the REVs is compared with analytical solutions of the Ergun equation or Darcy–Forchheimer law. The good agreements demonstrate the validity of the numerical method to simulate the macroscopic flow behavior in porous media. In addition, with the assistance of a scientific parallel computational library, PETSc, good parallel performances are achieved. Finally, the IB method is extended to simulate species transport by coupling with the REV flow simulation. The species sorption behaviors in an REV with impermeable/solid and permeable/microporous materials are then studied.