Two-dimensional measurements of magnetron discharge plasma parameters are used to calculate the forces applied to an isolated nanoparticle in conditions where nanoparticles are produced from cathode sputtering. Plasma spatial inhomogeneities, which are specific to magnetron discharges, also induce inhomogeneities in the charging mechanism and applied forces. It is shown that the nanoparticle transport is due to electric, thermophoretic and ion drag forces, and that the dominant one proportional to the nanoparticle size varies according to position. For a given plasma, these spatial differences explain the segregation of size in the nanoparticle deposits, which are observed inside the device.