Sedimentation velocity experiments on two TiO2 model colloids with similar properties but different surface structures were performed as a function of the solution pH in order to differentiate between similar size particles. The particle sedimentation velocity is highly sensitive to the surface structure, which is indicative of the exposed crystal face of the nanocrystals. Increase of the pH from 1 to 3 resulted in aggregation of all particles in one sample, whereas only partial aggregation occurred for the other, although the zeta-potential of both samples is almost identical in that pH range indicating particle stability. Although the particles are not distinguishable by the conventional methods for particle charge determination, they are clearly different in terms of their sedimentation coefficient distributions. Furthermore, analytical ultracentrifugation (AUC) reveals a dependence of the onset of large aggregate formation on the particle surface. This suggests that AUC has the potential to quantitatively determine differences in the particle surface structure even for polydisperse samples with constant average charge where conventional zeta-potential measurements yield only a constant average value. As ultracentrifugation yields distributions, we further discuss whether a combination with a second independent method like flow-field-flow fractionation can yield particle size and charge distributions in a global analysis approach.