Waterflooding is one of the geotechniques used to recover fuel sources from nanoporous geological formations. The scientific understanding of the process that involves the multiphase flow of nanoconfined fluids, however, has lagged, mainly due to the complex nanopore geometries and chemical compositions. To enable the benchmarked flow of nanoconfined fluids, architected geomaterials, such as synthesized mesoporous silica with tunable pore shapes and surface chemical properties, are used for designing and conducting experiments and simulations. This work uses a modified many-body dissipative particle dynamics (mDPD) model with accurately calibrated parameters to perform parametric flow simulations for studying the influences of waterflooding-driven power, pore shape, surface roughness, and surface wettability on the multiphase flow in heptane-saturated silica nanochannels. Remarkably, up to an 80% reduction in the effective permeability is found for water-driven heptane flow in a baseline 4.5-nm-wide slit channel when compared with the Hagen–Poiseuille equation. In the 4.5-nm-wide channels with architected surface roughness, the flow rate is found to be either higher or lower than the baseline case, depending on the shape and size of cross sections. High wettability of the solid surface by water is essential for achieving a high recovery of heptane, regardless of surface roughness. When the solid surface is less wetting or nonwetting to water, the existence of an optimal waterflooding-driven power is found to allow for the highest possible recovery. A detailed analysis of the evolution of the transient water–heptane interface in those nanochannels is presented to elucidate the underlying mechanisms that impact or dictate the multiphase flow behaviors.