Solvent plays an important role in the relative motion of nanoscopic bodies, and the study of such phenomena can help elucidate the mechanism of hydrophobic assembly, as well as the influence of solvent-mediated effects on in vivo motion in crowded cellular environments. Here we study important aspects of this problem within the framework of Brownian dynamics. We compute the free energy surface that the Brownian particles experience and their hydrodynamic interactions from molecular dynamics simulations in explicit solvent. We find that molecular scale effects dominate at short distances, thus giving rise to deviations from the predictions of continuum hydrodynamic theory. Drying phenomena, solvent layering, and fluctuations engender distinct signatures of the molecular scale. The rate of assembly in the diffusion-controlled limit is found to decrease from molecular scale hydrodynamic interactions, in opposition to the free energy driving force for hydrophobic assembly, and act to reinforce the influence of the free energy surface on the association of more hydrophilic bodies.