With recent advances in calculation methods, the external factors that affect slope stability, such as water content fluctuations and self-configuration, can be more easily assessed. In this study, a three-dimensional finite element strength reduction method was used to analyze the stability of three-dimensional slopes under fluctuating water conditions. Based on soil parameter variations in engineering practice, the calculation models were established using heterogeneous layers, including a cover layer with inferior properties. An analysis of seepage, deformation and slope stability was carried out with 27 different models, including three different slope gradients and nine different corner angles under five different hydraulic conditions. The failure mechanism has been shown to be closely related to the change in matric suction of unsaturated soils and the geometric slope configuration. Finally, the effect of geometry (surface shape, turning corner and slope gradient) and water (fluctuations) on slope stability are discussed in detail. Emphasis is given to comparing safety factors obtained considering or ignoring matric suction.