Iron oxide magnetic nanoparticles, in ferrofluids or as magnetic microspheres, offer magnetic maneuverability, biochemical surface functionalization, and magnetic relaxation under the influence of an alternating field. The use of these properties for clinical applications requires an understanding of particles, forces, and scalar transport at various length scales. This review explains the behavior of magnetic nano- and microparticles during magnetic drug targeting and magnetic fluid hyperthermia, and the microfluidic transport of these particles in bioMEMS (biomedical microelectromechanical systems) devices for ex vivo therapeutic and diagnostic applications. Magnetic particle transport, the momentum interaction of these particles with a host fluid in a flow, and thermal transport in a particle-infused tissue are characterized through the governing electrodynamic, hydrodynamic, and scalar transport equations.