Water inrush during the excavation of mines or mining is one of the great challenges in underground engineering work in China. To prevent and/or mitigate water inrush, natural sedimentary rocks with low-permeability, which include the mudstone and sandstone found in underground excavations, are exceptional materials for geological barriers. The aim of this work is to therefore investigate the hydraulic properties of sedimentary rocks in a deep tunnel, with the application of high-pressure packer tests (HPPTs). The experimental results indicate that both the mudstone and sandstone are low permeability. The measured injection pressure-flow rate (P-Q) can be divided into two phases: Phase I – a flow that is Darcian with a linear relationship, and Phase II – changes in the flow pattern with an exponential relationship. Water injection primarily triggers fracture dilation, and then results in an evident increase in hydraulic conductivity. The hydraulic conductivity versus water pressure distribution phase can be considered as three flow phases: the initial flow phase, initiation of flow communication phase, and non-steady state flow phase. The calculated original fracture apertures in mudstone and sandstone are, respectively, 0.37 and 0.33 mm. Furthermore, a conceptual model with two phases of fracture aperture versus water pressure is proposed.