The manipulation of matter at the nanoscale has unleashed a great potential for engineering biomedical drug carriers, but the transport of nanoparticles (NPs) under nanoscale confinement is still poorly understood. Using colloidal physics to describe NP interactions, we have computationally studied the passive transport of NPs using experimentally relevant conditions from bulk into a nanochannel of 60-90 nm height. NP size, channel height, and the Debye length are comparable so that changes in nanoscale dimensions may induce substantial changes in NP transport kinetics. We show that subtle changes in nanochannel dimensions may alter the energy barrier by about six orders of magnitude resulting in different NP penetration depths and diffusion mechanisms: ballistic, first-order and quasi zero-order transport regimes. The analysis of NP diffusion by continuum methods reveals that apparent diffusivity is reduced by decreasing channel size. The continuum finite element (FE) numerical method reproduced the colloidal model results only when surface interactions were accounted for. These results give a new insight into NP passive transport at the boundaries of nanoconfined domains, and have implications on the design of nanoscale fluidics and NP systems for biomedical and engineering applications.