A comprehensive understanding of molecular transport within nanoporous materials remains elusive in a broad variety of engineering and biomedical applications. Here, experiments and atomistic simulations are synergically used to elucidate the non-trivial interplay between nanopore hydrophilicity and surface barriers on the overall water transport through zeolite crystals. At these nanometre-length scales, these results highlight the dominating effect of surface imperfections with reduced permeability on the overall water transport. A simple diffusion resistance model is shown to be sufficient to capture the effects of both intracrystalline and surface diffusion resistances, thus properly linking simulation to experimental evidence. This work suggests that future experimental work should focus on eliminating/overcoming these surface imperfections, which promise an order of magnitude improvement in permeability.