Many leading-edge advances in the energy, bioengineering, transducers and data storage domains involve the development of magnetic nanostructures. Remote, tunable control of such nanostructures, e.g., nanofluids, is of high importance, and can be achieved by the interaction of uniform magnetic fields with magnetic nanofluids. Magnetic nanofluids consist of functionalized magnetic nanoparticles suspended in suitable carrier fluids. Such nanofluids have been developed for remote actuation, wireless control and easy micromixing in Lab-on-a-chip devices. Spreading of such nanofluids in three-stream micromixer channels was studied, which is useful in applications where control of fluid-fluid interface is desired, e.g., cell sorting, micromixers or micro-chemical reactors. The instability conditions of such nanofluids and their dependence on their physical properties were also investigated and compared to experimental results. Our multi-physics model, combining magnetic and fluidic analysis, showed, for the first time, excellent agreement between theory and experiment.