Has anyone had experience in using FEFLOW to calculate water levels in
surface water bodies?

Usually surface water bodies are included in groundwater models as head
dependent boundary conditions. In other words the water levels in lakes
or ponds are specified in the model input. However in many instances
it would be useful to use the model to caluclate the water levels in
the lake, pond or void. In the past we have addressed this problem by
including the size and shape of void in the model grid structure and
defined hydraulic parameters representative of a surface water body (ie
extremely high hydraulic conductivity, storage of 1.0 and recharge
defined as the excess of rainfall over evaporation) to the volume of
the void.

Is there a more sophisticated solution available in FEFLOW?

Cheers