Water transport is one of the major factors responsible for moisture damage in asphalt pavements. To study the thermodynamics and kinetics of water transport in bitumen and to uncover microscale mechanisms of moisture-induced damage, molecular dynamics simulations were performed for up to 600 ns for water–bitumen systems with realistic water contents that varied from 0 to 1.76 wt%. Hydrogen bonding interactions and clustering of water molecules at various combinations of temperature and water content were investigated, and their effects on the self-diffusion coefficient of water and bitumen properties are computed and discussed. It is shown that the saturated water concentration in bitumen is small, especially at low temperatures, and additional water molecules tend to form large water clusters via hydrogen bonding, indicating micro-phase separation of the water and bitumen phases inside the simulation box. Hydrogen bonding and water clustering play a crucial role on the magnitude of the self-diffusion coefficient of water. Physical properties of bitumen that include viscosity and cohesive energy are affected by water. The presence of large water clusters is indicative of how degradation in cohesion is observed on the microscale.