Water flow in a nanoscale channel is known to be affected by strong water-wall interactions; as a result, the flow considerably deviates from the conventional continuum flow. Nanochannel with a sudden contraction or expansion is the most fundamental morphological nanostructure in many nanoporous systems such as shale matrix, mudrock, membrane, etc. However, the nanoconfinement effects of water flow in nanoporous systems and its effect on macroscopic flow behavior are still evolving research topics. In this work, our recently developed pore-scale lattice Boltzmann method (LBM) considering the nanoscale effects is extended to directly simulate water flow in nanoporous systems. The results show that the flow rate is dramatically decreased in hydrophobic nanopores because of additional flow resistances at the contraction and expansion junctions. This indicates that the bundle of capillary models or the permeability averaging method overestimates the water flow rate in nanoporous media if the contraction/expansion effects between different nanopores are ignored. This work highlights the importance of wettability of the nanochannel in the determination of dynamic water flow behaviors in the contraction/expansion nanosystem. Other important aspects, including velocity distribution, flow patterns, and vortex characteristics as well as pressure variation along the flow direction, are for the first time revealed and quantified. Large differences can be found comparing gas or larger-scale water flows through the same system. A new type of pressure variation curve along the axis of flow direction is found in the hydrophobic nanochannel with a sudden contraction/expansion. This work provides the fundamental understanding of water transport through the nanoscale system with contraction and expansion effects, giving implications to a wide range of industry applications.