I cannot specifically answer your question (because I don't know) but I do walk past there now and again (was just up the coast yesterday).
The geology of the island is a little "odd" in that it has a hugely varied geological structure for such a small mass of land. Interestingly, Moelfe is one of the very few coastal areas in limestone where a rising is possible.
Didn't Gus Horsley have an item in Descent about this?(ages ago) I think there was some depression just inland at Moryn (or Morcyn) that he thought resurged on the beach?
My own hunch is that something might be found along the escarpment along the Lligwy. At this point the limestone sits on a basal sandstone, and dips south east. In a number of places streams or valleys cutting up dip are found, and there may be underground streams cutting up dip as well.