The present work deals with experimental studies to examine the theoretical model of thermodiffusion of electrically charged nanoparticles. Three different ionic magnetic colloid samples have been synthesized and profoundly analyzed. The theoretical model is a classical one, based on the calculation of the temperature and the electric potential distribution around nanoparticles. The discrepancy between experimental data and theory turns out not to exceed 20%. We focus on applying different approximations between calculated electrical double layer in the theoretical model and experimental determination of the surface charge density of colloidal particles. We assume this is the main reason for obtained discrepancy.