The self-assembly and deposition mechanisms of nanoparticles in droplets on a substrate are of significant importance in many inkjet printing-based industrial applications such as microelectronics, display systems, and paint manufacturing. However, a comprehensive investigation into the velocity field of fluid and its accompanying particle transport behavior in injected droplets undergoing immediate evaporation has not been conducted. In this study, we describe the underlying mechanisms of the self-assembly and deposition behavior of nanoparticles in inkjet-printed, evaporating droplets by visualizing the internal fluid flows. We additionally characterize the relationship between the internal fluid flows and nanoparticle patterns by changing not only the wettability and temperature of the substrate, but also the chemical composition of nanoparticle suspensions. We verify that Marangoni flow generated on a hydrophobic PDMS substrate with a contact angle (CA) of >90° helps the formation of dome-shaped nanoparticle structures, while radially outward flow generated on a hydrophilic glass substrate with a CA of <10° produces either mono-layered and flat, or ring-shaped nanoparticle structures, depending on the number density of the suspension. The presented characterization results provide not only valuable mechanistic insights, but also practical guidelines for inkjet printing-based nanoparticle applications. © 2017 Elsevier B.V.