Cellulose nanocrystals (CNCs) are biologically derived nanoparticle of significant scientific interest due to their liquid crystalline properties with the ability to self-assemble into chiral nematic domains, called tactoids. We have investigated the process by which structural properties can be modified through hydrodynamic alignment and the addition of a salt (NaCl) solution, using in-situ scanning SAXS, illustrating the time scales involved in the mixing and subsequent transition.Our experimental setup consists of a device wherein two pairs of perpendicular flows first accelerate and align a core flow of CNCs. The first step is an injection with water and the second step constitutes a NaCl solution. A steady-state core flow of CNCs moves downstream with a constant velocity and negligible shear, so-called plug flow, allowing for a trivial conversion from downstream positions to mixing times.The CNCs in the core flow undergo a phase transition as it passes through the channel, making them initially aligned with the first shear flow, and with their nematic structure intact. However, upon contact with NaCl in the second perpendicular flow, the sizes of individual tactoids are reduced, triggering an increase of Brownian motion and an eventual aggregation into a gel state. From the SAXS data, we can track both alignment and the CNC arrangement inside the tactoids. This allows a detailed insight into the phase transition from a cholesteric liquid state to a more isotropic formation.The study is aimed at fundamental understanding of the intricate interplay of hydrodynamic forces, Brownian motion, ion diffusion and CNC-ion interactions. The process here is dependent on the flow rate, CNC concentration, and ion concentration, which could be controlled to obtain desired properties. We thus envision that the fundamental knowledge from this project can lead to new strategies for designing processes for new advanced nanocellulosic materials with tunable properties.