Sandy natural levee deposits have been pointed out to provide seepage paths under river levees, which are largely related to the underseepage problems. However, few attempts have been taken to quantitatively study the relationship between the natural levees and the leakages in river levees. To capture the features of real natural levees, statistical studies are performed on the geometry and hydraulic conductivity of the micro-topographies along the Kinu River in Japan. By setting cases based on the retrieved data, a parametric study on the geometric and hydraulic parameters is performed by finite element seepage analysis. As a result, the embankment sitting on the landside of the natural levees is identified to be susceptible to leakages. In addition, rainfall and flooding are distinguished as the two driving forces of leakages depending on the hydraulic conductivity of the embankment bodies and the underneath foundations. The sandy natural levee deposits, with relatively high hydraulic conductivity, providing seepage paths for the under seepage, may magnify the effects of the seepage driven by the flooding, and lead to the classical backward erosion piping. Discussion and comments are addressed for the existing engineering practice in Japan.