Due to climate change over the last decades, flood events in Hungary and other European countries have become increasingly frequent, with greater intensity and duration. These changes have impacted flood protection levees. A long-duration flood allows water to seep into the levees, saturating them and maximizing the potential for damage. Seepage through earthen levees is often observed during floods and can lead to levee failure if combined with internal erosion. This study assesses the levee vulnerability relative to seepage by considering the characteristic time scales of the seepage phenomena and the main factors driving them. The procedure is applied to the Körös sub-basin (Hungary), a site that has shown a continuous trend of increased water levels in recent years. Along the critical section of the levee, a comprehensive site investigation was carried out. The analysis has shown that hydraulic conductivity is the most significant parameter when considering seepage for levees along the Kettős-Körös River. The investigated dyke geometry shows higher vulnerability to lower water levels associated with a longer duration of flood water levels.