Three-dimensional spheroid arrays represent in vivo activity better than conventional 2D cell culturing. A high-throughput microfluidic chip may be capable of depositing cells into spheroid arrays, but it is difficult to regulate the path of individual cells for deposition. Droplets that encapsulate cells may aid in facilitating cell delivery and deposition in the return bend of a microfluidic chip. In this study, a low-cost method for fabricating polymer-cast microfluidic chips has been developed for rapid device prototyping. Computational fluid dynamic (CFD) simulations were conducted to quantify how a change in geometry or fluid properties affects the dynamics of a droplet. These simulations have shown that the deformation, velocity, and trajectory of a droplet are altered when varying the geometry and fluid properties of a multiphase microfluidic system. This quantitative data will be beneficial for the future design of a microfluidic chip for cell deposition into 3D spheroid arrays.