We investigate the effects of hydrodynamic interactions on the dynamics of polymer chains in nonuniform geometries using a hybrid lattice-Boltzmann algorithm. One such geometry is the entropic trap device which consists of wide and narrow sections, with the narrow section usually smaller than the radius of gyration, Rg, of the polymer chain. The flow of polymers in such geometries can be driven by either an electric potential, a uniform body force, or a hydrodynamic flow field. We study the effects of the lateral position and width of the narrow section, the field and flow strength, and chain length. The effects of hydrodynamic interactions between polymer segments are also examined by comparing results with and without hydrodynamic interactions. We will discuss the separation efficiency as well as, advantages and disadvantages of these geometries.