Abstract The paper deals with the relatively weak permeable layer in a layered structure of a slope rock mass and its effect on groundwater behaviour in the rock mass. When the whole groundwater table is declined in such type of slope rock mass, the permeability of the relatively weak permeable layer in the middle will be several times lower than that of the upper and lower permeable layers and consequently the water level in layers of different permeability will fall in different rates which will lead to a discontinuous phenomenon of the water body. A method of finite element simulation on a vertical two‐dimensional profile is suggested for the study of the phenomenon and its application to practical situation is described. The calculation result shows that the existing weak permeable layer in a layered slope rock mass exerts unnegligible influence on the variation of water level in the rock mass of a slope. The result also proves the applicability of the finite element simulation method.