You can link the parameter source/sink or in/out-flow on top/bottom to a mathematical expression (or Python function). The expression will be evaluated before the time step execution, so you can basically modify anything as you want, e.g. using elemental user distributions with potential recharge factors.
There are different ways to introduce the temporal data in FEFLOW, I will recommend you to take a look on http://www.feflow.info/html/help75/feflow/09_Parameters/Material_Properties/time_varying_materials.html
Cheers, Carlos