AbstractWater flow in nanoporous structures in shale strongly depends on water‐pore wall interactions; specifically, water‐pore wall interactions may influence flow more than water‐water interactions. Because of strong water‐pore wall interactions, the models that govern flow in nanoporous structures deviate from conventional continuum flow models such as the Darcy equation. We develop a novel lattice Boltzmann model to study water flow in nanoporous structures rendered from shale samples. First, we reconstruct three‐dimensional (3‐D) stochastic digital models based on composite shale samples that include hydrophobic organic matter (OM) and hydrophilic clay minerals. In the reconstructed digital models, we use pore size/shape distributions, porosity, and mineralogy from experiments. Then we use lattice Boltzmann models to model water flow through nanoporous structures (OM and clay) of the reconstructed shale sample, and we upscale the results to a microporous structure of composite shale containing OM, clay, and interpores associated to other minerals. The results show contraction/expansion effects of pore‐throat‐pore systems in nanoporous OM weaken the hydrophobicity‐induced slippage effect on total water flow. In nanoporous clay, the swelling effect predominates and diminishes water slippage effects on water flow. The work also highlights the importance of (1) the accuracy of reconstructed 3‐D pore networks in terms of pore connectivity, shape, and tortuosity in individual systems of OM and clay and (2) the role of OM nanopores in connecting isolated micropores to total water flow through the composite shale system.