The need to understand and describe permeation through membranes has driven the development of many well-established transport models. The modeling parameters such as solubility, diffusivity, and permeability represent the intrinsic nature of molecular interactions between membrane and permeants. In this study, we report a simulation and analysis methodology for liquid permeation. On the basis of a single simulation of liquid sorption process into a membrane, the solubility and diffusivity are estimated simultaneously; then, the permeability is predicted by the solution-diffusion model. The methodology is applied to water permeation through two representative membranes: a polymer of intrinsic microporosity (PIM-1) and a zeolitic imidazolate framework (ZIF-96). For amorphous PIM-1 membrane, the predicted water permeability agrees perfectly with simulation. For crystalline ZIF-96 membrane, water permeability is fairly well predicted. Furthermore, water dynamics in the membranes is analyzed by simulation trajectories and water structure is characterized by hydrogen bonds. Together with these microscopic insights, this study provides a simple theoretical approach to quantitatively describe water sorption, diffusion,and permeation, and it can be further applied to other liquid permeation (e.g., organic solvent nanofiltration).