The ability of heavy metals to accumulate in living organisms, combined with the fact that they are not biodegradable, necessitates an expansion and improvement of the existing water purification methods. An effective mixing of contaminated water with heavy metals and magnetic nanoparticles is crucial for water treatment applications. In the present work, electromagnetic and shear mixing are combined to explore optimization mixing strategies. Mixing is studied through simulations under various initial conditions for two streams that are loaded with nanoparticles and one contaminated water stream that lies between the nanoparticle streams. In the present work, magnetic mixing is superimposed with a time-modulated gradient external magnetic field. The results show that as the radius ratio between the nanoparticles and the heavy metals increases, the external magnetic field is more effective insofar as the mixing of the nanoparticles is concerned. Moreover, for simulations where the radius ratio is higher or equal to 10, an effective mixing is achieved. By comparing the velocity ratios, a better mixing is achieved in the case of higher velocity ratios. Also, minor effects on mixing are observed by comparing the ratios Vp/Vc = 10 and Vp/Vc = 20.