Pure geological modelling is typically done in other software, such as Leapfrog Hydro. FEFLOW can be used to simulate groundwater flow based on a geological model (that in simpler cases can be set up directly in FEFLOW). Groundwater flow can - of course - also include submarine springs. In case you refer to the marine side of the spring rather than the groundwater side, have a look at the capabilities of MIKE 21 and MIKE 3.
