Levees are earth structures used for flood protection. Due to their easy availability and low permeability, clays are the most common material used for the construction of levees. Clays are susceptible to desiccation cracks when subjected to long dry spells during summers. There has been an increased interest in studying the occurrence of cracks in soil mass. In particular, many experimental investigations for soils have been undertaken to learn about the crack pattern in earth embankment. However, there is a dearth of work that focuses on the numerical modeling of desiccation cracks effects on levees. This study has been undertaken to analyze the effect of desiccation cracking on the hydraulic behavior of an earth embankment under flooding conditions. A numerical model was developed using the finite element package CODE_BRIGHT. The model was validated from the data obtained from a small scale embankment experiment under controlled environmental conditions. As the phenomenon of desiccation cracking is highly random, a simple random model was developed to capture the variability in crack geometry. The random crack geometry was then passed on to the finite element mesh, so that a probabilistic analysis can be carried out using a Monte Carlo approach, for assessing the embankment’s integrity. The results obtained from the analysis such as time to steady state saturation and steady state flow rate at the outward slope were very interesting to study and provided an insight on the effect of desiccation cracks on unsaturated earth embankments.