During the excavation of a water-conveyance tunnel in Tertiary soft rocks in China, significant deformation of the surrounding rocks and damage to the support were observed. Substantial horizontal deformation, reaching magnitudes of meters, was observed in the right side wall after a certain period of tunnel excavation. Extensive investigations, including field surveys, monitoring data analysis, laboratory tests, and numerical simulations, were conducted to understand the underlying mechanisms of this large deformation. The section of the tunnel with large deformation consisted of Tertiary sandy mudstone, mudstone interbedded with marl, and glutenite. Laboratory tests and mineral composition analysis revealed that the sandy mudstone and mudstone interbedded with marl exhibited low strength, which was closely related to the water content of the rock specimens. The compressive strength gradually decreased with increasing water content, and when the water content of mudstone interbedded with marl reached 26.96%, the uniaxial compressive strength decreased to only 0.24 MPa. Additionally, sandy mudstone and mudstone interbedded with marl contained a significant amount of hydrophilic minerals, with montmorillonite constituting 30% and 34% of the two rock samples, respectively. The tunnel passed beneath a perennially flowing gully, and a highly permeable glutenite layer was present in the middle of the tunnel. This resulted in groundwater seepage from the inverted arch during excavation, leading to the softening effect on the mudstone interbedded with marl in the lower part of the tunnel. Through numerical simulation and back-analysis techniques, the varying degrees of softening induced by groundwater were quantitatively analyzed in the surrounding rocks on the left and right sides. The study revealed that the large deformation of the tunnel was triggered by two factors: the plastic flow caused by tunnel excavation under the low strength of the surrounding rocks and the softening effect of groundwater. The damage to the support system was primarily attributed to the squeezing and swelling deformation of the surrounding rocks and the non-uniform deformation between different rock layers.