Natural soils contain a certain amount of salt in the form of dissolved ions or electrically charged atoms, originated from the long-term erosion by acidic rainwater. The dissolved salt poses an extra osmotic water potential being normally neglected in laboratory measurements and numerical analyses. However, ignorance of salinity may result in overestimation of stability, and the design may not be as conservative as thought. Therefore, this research aims to first experimentally examine the influence of pore water salinity on water retention curve and saturated permeability of natural dispersive loess under saline and desalinated conditions. Second, the measured parameters are used for stability analyses of a railway embankment in an area subjected to regional rainfall incident. Eventually, a numerical parametric study is carried out to explore the significance of different rainfall schemes, construction patterns, and anisotropic permeability on the factor of safety. Results reveal that desalinization suppresses the water retention capability, which in turn results in a tremendous declination of unsaturated hydraulic conductivity. Despite the natural saline embankment, rainfall can hardly infiltrate into the desalinated embankment due to the lower conductivity. Therefore, the factor of safety for natural saline conditions drops notably, while only marginal changes occur in the case of the desalinated embankment.