You can now use arbitrary expressions for recharge calculation in
FEFLOW. On
http://www.wasy.de/english/produkte/feflow/howto/video_evapotranspiration.htm
you find an example for a depth-to-groundwater dependent ETP for some
different zones in the model area. There's no limit in complexity of
the equations used or in the number of the input parameters.
Good luck!
Peter Schätzl
Product manager FEFLOW