The combination of nanotechnology and microfluidics may offer an effective water and wastewater treatment. A novel approach combines the use of magnetic particles which can capture heavy metal impurities in microfluidic ducts. The purpose of this study is to investigate the mixing mechanism of two water streams, one with magnetic particles and the other with wastewater. The optimum mixing is obtained when particles are uniformly distributed along the volume of water in the duct for the combined action of a permanent, spatially and temporally aligned magnetic field. Results showed that mixing is enhanced as the frequency of the magnetic field decreases or its amplitude increases, while magnetic gradient is found to play an insignificant role in the present configuration. Moreover, for simulations with low frequency, the mean concentration of particles is found to be twice as high as compared to the cases with higher frequency. Optimum distribution of particles inside the micromixer is observed for the combination of 0.6 T, 8 T/m and 5 Hz for the magnetic magnitude, gradient and frequency, respectively, where concentration reaches the optimal value of 0.77 mg/mL along the volume of the duct.