Flooding window wells can leak through your basement windows and cause major flooding in your home. What is the solution to stop your window wells from filling up with water? If your window wells are filled up with water, there are two primary causes to the problem. One may be that you window wells do not have plastic covers, and when it rains, the rate at which water goes directly into your window wells, and overflows into your home. The other cause of flooding window wells may be that the water table rises during rainstorms, and the water table rises to a point where it floods your window well.