Abstract The electrophoretic mobility of poly(N-isopropylacrylamide) and poly(N-isopropylacrylamide-co-acrylic acid) copolymer particles, as well as different core-shell microgel particles (neutral core with charged shell and charged core with neutral shell) was investigated as function of microgel swelling. The swelling of the microgels were varied with increasing the temperature. To interpret the experimental results, we used scaling arguments to show that due to the strong hydrodynamic interactions the inner part of the microgel particles are non-draining in low ionic strength media and only the outmost thin shell of the microgel contributes actively to the electrophoretic mobility. We found that the experimental results were in good agreement with the prediction of this model, while we found physical inconsistencies when the experiments were analysed in terms of the draining models often used in the literature.