The transport behavior of a system of gravitationally driven superparamagnetic colloidal particles is investigated. The motion of the particles through a narrow channel is governed by magnetic dipole interactions, and a layered structure forms parallel to the walls. The arrangement of the particles is perturbed by diffusion and the motion induced by gravity leading to a density gradient along the channel. Our main result is the reduction of the number of layers. Experiments and Brownian dynamics simulations show that this occurs due to the density gradient along the channel.