Effective hydraulic conductivity is typically used to evaluate groundwater flow in faulted/fractured media. Estimating effective hydraulic conductivity relies on modelling the transmissivity and hydraulic connectivity of faults/fractures using a large dataset. As an alternative to evaluating hydraulic connectivity, flow dimension is an easily available and quantitative indicator of fault/fracture hydraulic connectivity. However, the flow dimension has not been used as much quantitatively to evaluate the effective hydraulic conductivity. This study demonstrates how flow dimensions in poorly self-sealed faults directly relate to effective hydraulic conductivities. Effective hydraulic conductivities of massive siliceous mudstone of the Wakkanai Formation around the Horonobe Underground Research Laboratory (URL) in Japan were analysed by simulation with long-term (>10 years) data of hydraulic pressure and inflow during the construction and operation of the URL. The estimated effective hydraulic conductivities varied from c . 10 −8 to c . 10 −11 m s −1 with an increase in depth from c . 250 to c . 600 m. The fault local transmissivities and flow dimensions from packer tests varied from c . 10 −6 to c . 10 −10 m 2 s −1 and from c . 2.0 or more to c . 1.0 with increasing depth, respectively. When applying the Landau–Lifshitz–Matheron formula to calculate the fault effective transmissivities, these variations correlate well and the estimated effective hydraulic conductivities are sound.