Non-negligible internal erosion threatens deep foundation pit excavation safety and stability. A water-inrush incident in Guilin city, a typical karst area, is thoroughly analysed theoretically after revealing groundwater seepage effects on hydraulic conductivity, internal erosion degree and water-flooding probability. The distribution characteristics of the main granular soils at the site are examined. Internal erosion by suffusion of readily erodible gap-graded soil, widely distributed in situ, is specifically studied. The hydraulic conductivity of soil can be determined by the internal erosion extent, S (%), directly calculated by the effective particle size. Comparing the influences of different parameters on permeability, it is found that the formula with uniform coefficient Cu is more practical, because it is more applicable in gap-graded soil with a wide range of hydraulic conductivity, such as the permeability coefficient range of 10−6 to 101 cm/s. The permeability coefficient-based relationship between seepage velocity and hydraulic gradient is determined. By establishing and implementing a numerical model, the pore-pressure history in each excavation phase reveals that the pore pressure notably increases during excavation, especially in areas adjacent to ancient collapse bodies. Seepage flow driven by excess pore pressure potentially generates a penetrating flow upward through the overlaying soil, possibly triggering a water-inrush incident at a maximum seepage velocity of 8.0×10−1 cm/s. Several suggestions are proposed to prevent water-inrush incidents during deep foundation pit excavation in similar geological setting areas.