Evolution of microstructure and rheology during flow startup, and its connection to microscopic transport processes, is studied theoretically via active microrheology. At steady state, the balance between entropic, hydrodynamic, and other forces changes with flow strength, producing sustained microstructural asymmetry and non-Newtonian rheology. However, the transition from equilibrium to steady flow is sometimes marked by overshoots in viscosity that suggests a temporally evolving competition between these rate processes. Here, we formulate and solve a Smoluchowski equation for the time-dependent evolution of particle microstructure induced by the motion of a colloidal probe driven through a bath of colloidal spheres. The structure is then utilized to compute the time-dependent microviscosity. Brownian diffusion always sets short-time particle dynamics, which hinders maturation of the boundary layer. The disparity in Brownian and advective transport rates produces a reversal from flow thinning to flow thickening during startup, revealing that non-Newtonian flow phenomenology is not instantaneously established. (C) 2018 American Institute of Chemical Engineers