The Cebala-Borj Touil (Cebala) Plain in Tunisia is a large perimeter with an area of 3,200 ha. In 1990, a drainage and irrigation system was installed. The groundwater system is complex due to the proximity to the sea, the low slope, and the low performance of natural drainage. It is characterized by shallow groundwater and soil water logging. The flooded area is controlled by natural and artificial factors. The natural parameters are the flat slope and the soil texture. The man-made problems are caused by inappropriate irrigation and drainage deficiency. The numerical groundwater flow simulation model FEFLOW (Finite Element Subsurface Flow System) was used to simulate the groundwater depth variability. The calculated water table depth ranged from less than 0.5 m from the ground surface to more than 8 m. Based on the calibrated model, several management scenarios were investigated to study the possibilities to mitigate the problem of water logging in the perimeter. The model results showed that improving the drainage efficiency and reducing the irrigation amounts could solve the water logging problem, but not entirely. For the low flooded parts, a pumping option could be considered. The final management scheme might include the combination of all the tested management scenarios.