The effect of polymer-clay specific interactions, diffusion and hydrodynamics on the structure development in clay-polymer nanocomposites were studied on a model system made of PDMS-F matrix filled with 2wt% of Cloisite 30B, where F is the nature of the attached functional group with increasing intensity of polymer-C30B specific interactions. The steps of clay dispersion and distribution were followed-up by in-situ XRD and light scattering during flow. The obtained results allowed drawing a qualitative picture of structure development that was quantitatively described DLVO theory coupled with diffusional and rheokinetic models.