If you use the In-/Outflow on Top/bottom parameter in a 3D model, FEFLOW will assume a concentration of 0 mg/l for recharge. When doing a cross-sectional model, however, you'll have to use a Fluid-flux BC for recharge, and this will (by default) NOT assume freshwater, but a gradient of 0, meaning that recharge will enter with the current concentration of the node the BC is set to.