Seepage is a sub-process of high relevance for a stability statement, because the phreatic line separates the cross-section into the water-saturated and the unsaturated cross-sectional part. In stationary cases, the phreatic line is imprinted into homogeneous systems by the outer cubature. In transient cases and the analysis of structured designs, its position depends on the material’s saturated permeability. However, the saturated permeability is a spatially scattering and therefore uncertain quantity which should be considered as such. This paper presents a methodology to incorporate the phreatic lines probabilistically in river levee cross sections and applies to standard designs. Using input distributions, the position of the seepage line is analytically determined as an uncertain quantity. By means of a Monte-Carlo simulation it is then evaluated in the form of undercutting probabilities of discrete phreatic lines. Subsequently, the effect of uncertain phreatic lines on the stability of levees is illustrated by the results of a reliability analysis. The results show a variability in the stability statement which is quantified by the failure probability. In the end, not only the input distributions of the saturated permeability are decisive for the quality of the results, but also the distributions of further soil mechanical parameters. Therefore, it is recommended to summarize experiences with soil mechanical parameters in an (inter)national database to feed probabilistic parameter studies.