Abstract. The hydraulic conductivity of unsaturated peat soil is controlled by the air-filled porosity, pore size and geometric distribution as well as other physical properties of peat materials. This study investigates how the size and shape of pores affects the flow of water through peat soils. In this study we used X-ray Computed Tomography (CT), at 45 μm resolution under 5 specific soil-water pressure head levels to provide 3-D, high-resolution images that were used to detect the inner pore structure of peat samples under a changing water regime. Pore structure and configuration were found to be irregular, which affected the rate of water transmission through peat soils. The 3-D analysis suggested that pore distribution is dominated by a single large pore-space. At low pressure head, this single large air-filled pore imparted a more effective flowpath compared to smaller pores. Smaller pores were disconnected and the flowpath was more tortuous than in the single large air-filled pore, and their contribution to flow was negligible when the single large pore was active. We quantify the pore structure of peat soil that affects the hydraulic conductivity in the unsaturated condition, and demonstrate the validity of our estimation of peat unsaturated hydraulic conductivity by making a comparison with a standard permeameter-based method. Estimates of unsaturated hydraulic conductivities were made for the purpose of testing the sensitivity of pore shape and geometry parameters on the hydraulic properties of peats and how to evaluate the structure of the peat and its affects on parameterization. We also studied the ability to quantify these factors for different soil moisture contents in order to define how the factors controlling the shape coefficient vary with changes in soil water pressure head. The relation between measured and estimated unsaturated hydraulic conductivity at various heads shows that rapid initial drainage, that changes the air-filled pore properties, creates a sharp decline in hydraulic conductivity. This is because the large pores readily lose water, the peat rapidly becomes less conductive and the flow path among pores, more tortuous.