Nanoparticle spray deposition finds numerous applications in pharmaceutical, electronics, manufacturing, and energy industries and has shown great promises in engineering the functional properties of the coated parts. However, current spray deposition systems either lack the required precision in controlling the morphology of the deposited nanostructures or do not have the capacity for large-scale deposition applications. In this study, we introduce a novel spray system that uses supercritical CO2 to assist the atomization process and create uniform micron-size water droplets that are used as cellulose nanocrystal (CNC) carriers. CNCs are selected in this study as they are abundant, possess superior mechanical properties, and contain hydroxyl groups that facilitate interaction with neighboring materials. We fundamentally investigate the effect of different process parameters, such as injection pressure, gas-to-liquid ratio, the axial distance between the nozzle and substrate, and CNC concentration on the final patterns left on the substrate upon evaporation of water droplets. To this end, we show how tuning process parameters control the size of carrier droplets, dynamics of evaporation, and self-assembly of CNCs, which in turn dictate the final architecture of the deposited nanostructures. We will particularly investigate the morphology of the nanostructures deposited after evaporation of micron-size droplets that has not been fully disclosed to date. Different characterization techniques such as laser diffraction, polarized microscopy, and high-resolution profilometry are employed to visualize and quantify the effect of each process parameter. Numerical simulations are employed to inform the design of experiments. Finally, it is shown that the fabricated nanostructures can be engineered based on the size of the carrier droplets controlled by adjusting spray parameters and the concentration of nanoparticles in the injected mixture. Process parameters can be selected such that nanoparticles form a ring, disk, or dome-shaped structure. Moderate operational conditions, simplicity and time efficiency of the process, and use of abundant and biodegradable materials, i.e., water, CNC, and CO2 promote the scalability and sustainability of this method.