A novel method of dynamically and selectively controlling the diffusion of molecules using aggregation of ferrofluid is proposed. This method can be used to mask specific locations on a surface for combinatorial chemistry or to restrict diffusion of molecules in selected areas in a microfluidic device. This method works by using the controlled aggregation of stabilized l0nm diameter iron oxide particles (ferrofluid) to slow the diffusion of molecules in a similar manner as to how a porous media restricts diffusion. Dynamic aggregate formation is controlled by a magnetic pattern on a substrate in conjunction with an external field. The external magnetic field bias applied to the system causes ferrofluid to aggregate only in designated areas around the magnetic patterns thereby slowing diffusion through the areas where the aggregate clouds have formed. © 2005 Materials Research Society.