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Surface functionalized magnetic nanoparticles (MNPs) are appealing candidates for analytical separation of heavy metal ions from waste water and separation of actinides from spent nuclear fuel. This work studies the separation dynamics and investigates the appropriate magnetic-field gradients. A dynamic study of colloidal MNPs was performed for steady-state flow. Measurements were conducted to record the separation time of particles as a function of magnetic field gradient. The drag and magnetic forces play a significant role on the separation time. A drop in saturation magnetization and variation of particle size occurs after surface functionalization of the MNPs; these are the primary factors that affect the separation time and velocity of the MNPs. The experimental results are correlated to a theoretical one-dimensional model.