The design of tailor-made nanofluidic devices requires an extension of macroscale hydrodynamic theories for capillary impregnation (CI). Large-scale molecular dynamics (MD) simulations of a simple capillary pump consisting of a nanoscale gold slit attached to a liquid propane reservoir reveal that distinct finite-size-effects impact CI on the nanoscale. A continuum theory is derived that captures these finite-size-effects: properties of a prewetting monolayer, a related Navier-slip, nanoscopic contact angles and wall-induced oscillatory pressure fluctuations enter as non-heuristic atomistic input into the derivation of extended lubrication equations that exactly reproduce the capillary rise dynamics and menisci from our MD simulations. It turns out that impregnation in bare nanochannels can be significantly accelerated by the strong slip induced by a spreading precursor. As expected, this effect is absent in micron sized channels, where our extended continuum theory predicts a capillary dynamics that is already insensitive to all nanoscopic details at the contact line.