The service life and durability of concrete structures strongly depend on the transport properties of the concrete. Water permeability is one of the important indicators for durability of concrete. The water acts as a carrier of aggressive agents, such as chloride ions, sulphate ions and acid that can activate many chemical reactions, speeding up the degradation process of concrete structures. Pore structure is the most important characteristics controlling the transport properties of the hydrated cement paste. Hence, knowledge of the relationship between water permeability and pore structure of cement paste is needed for engineers. Owing to the pozzolanic reaction, fly ash can refine the pore structure of cement paste, eventually affect the water permeability. In this paper the effect of fly ash on the water permeability of cement paste is investigated at ages of the cement paste up to 2 years. The basic pore parameters of cement paste blended with fly ash were already discussed in previous study. This paper only investigates the pore parameters, such as capillary porosity, connectivity of the capillary pores, related to transport properties of cement paste. The results show that at later ages, such as 180 days, cement paste blended with fly ash is less permeable than pure Portland cement paste. This mainly results from the refinement of the pore structure caused by the pozzolanic reaction of fly ash. Based on the comprehensive comparison of the pore structure and the water permeability between ordinary Portland cement paste and cement paste with fly ash, the crucial pore parameter governing the water permeability of cement paste blended with fly ash is the Connectivity of the capillary pores. Capillary porosity is not the significant factor affecting the permeability of cement paste. The comparison obtained in this study enables a good understanding of fly ash incorporated in cement-based materials, and provides information for the use of fly ash in practice.