Hi Karanka
In reading your description again, it seems that you have recharge for introducing water to the model, but no mechanism for it to escape such as a boundary condition? This would explain excess saturation of the model domain.
You said that you had "entered no flow boundary conditions" on three sides? What about the fourth side? (Assuming it's rectangular).
Did you know that if you do nothing, then all external boundaries of the model are no-flow. Hence, you can't really "assign" a no flow boundary. It just is one until you assign a flow boundary. Perhaps you are assuming that water can leave through the fourth side when in fact it can't until you assign a type 1, 2 or 3 BC there...