Flocculated nanoparticle dispersions exhibit fractal-like microstructures in solution that evolve with the applied shear rate and stress. In this work we compare and contrast rheological, Rheo-SANS, and flow-USANS measurements of the evolving microstructure of two model colloidal and nanoparticle dispersions in the shear thinning and shear thickening regime. A near hard-sphere colloidal dispersion at high volume fraction is observed to exhibit interparticle structural rearrangements during shear thickening as observed during flow- USANS. The results are compared against theoretical and experimental expectations of hydrocluster formation. A commercial flocculated nanoparticle dispersion is found to exhibit thixotropy and shear thickening. Inter as well as intra particle rearrangement is observed during shear thinning and shear thickening. Comparison of the rheology and SANS measurements provides important insights into the interplay between structure in the dispersions and the measured thixotropy.