Groundwater seepage into a former mining site in Egypt is proposed for simulation. This site was used for Basalt extraction. After the mining activities had stopped a large open pit was left over and groundwater seeped into the pit forming a lake. The pit has a dimension of approximately 1200 × 600 × 30m. Because of the lack of field data, several scenarios may be hypothesized to explain the filling of these open pits with water. In this paper, one of these scenarios is studied. It is suggested that this water comes from an underneath confined aquifer. Through fractures in the host rock, water seeped upwards into the open pit. To estimate the rate at which water seeps into the lake, numerical study based on the finite element method is performed. Firstly, georeferencing of the site was performed using GIS. The boundary of the lake was then digitized and elevation contours was defined. These data was then imported into GridBuilder software to generate a two-dimensional triangular mesh which was then used by HydroGeoSphere software to build the three-dimensional mesh and solve the problem. It was found that the set of discrete fractures was insufficient to fill the lake in the time span that was actually elapsed to fill up the lake which is on the order of two to three years.