Clay suspensions present complex microstructures in different environments and deep understanding of such microstructures is crucial to control their flow properties. Their rheological profile is closely linked with the structural association (3-D network) of bentonite particles. Nanomaterials are considered very good candidates for smart fluids formulation which can improve the performance of conventional drilling fluids. Their incorporation in water-bentonite suspensions endow complex microstructures and hence complex rheological behavior, which is still under investigation. This study aims to explore the micro-mechanisms involved on shaping this rheological behavior with samples of 7 wt% water-sodium bentonite suspensions containing 0.5 wt% each of, commercial Fe3O4, commercial SiO2 NP and custom-made (bare or citric acid coated) Fe3O4 NP at alkaline pH. We tried to achieve this by combining macroscopic measurements (rheological measurements) with microscopic measurements (i.e. TEM). A comprehensive physico-chemical characterization of the materials and suspensions was performed using X-Ray Diffraction (XRD), X-Ray Fluorescence (XRF), N2 adsorption-desorption isotherms and Fourier-transform infrared spectroscopy (FTIR). An effective drying process was adopted using freeze-granulation and freeze-drying (FG-FD) techniques in order to capture as accurately as possible the evolved microstructures of these aqueous bentonite suspensions at the different temperatures (25–60 °C). The results indicated that all samples exhibited a yield stress followed by a shear thinning behavior. The three parameter Herschel-Bulkley model provided excellent fit of the experimental data for all samples. HR-TEM images revealed that the association of the nanoparticles with bentonite particles in different configurations plays a crucial role in their rheological characteristics with the charge and the coating of the added nanoparticles being important factors in determining the magnitude of the effects observed. We hypothesize that attractive magnetic forces between the magnetite nanoparticles may suppress the electrostatic repulsions and thus they may play a key role in promoting the observed aggregation of the nanoparticles which in turn plausibly affected their rheological profile. A thorough examination and understanding of the evolution of such complex inter-particle structures may lead towards an optimal rheology control of such suspensions in a wide range of applications.