Not explicitly, but I think it can be tied to the same reason they can't use the transporter. It is said that something about the planet's magnetic field is interfering with the transporters which is why they can't just beam Spock out while still under the ocean. Also, the magnetic field might have made studying the volcanic and seismic activity difficult from orbit. And considering starship hulls are constructed out of metals far more durable than anything WE can currently use, I have no issues with the Enterprise being under water, and I think Scotty was just being overprotective of his precious wee bairns.
Also, it took me several viewings of the crappy YouTube version to get what the heck McCoy was saying after Kirk stunned that thing. But you know, given Kirk's previous experiences with big animals, can you blame him for automatically stunning the thing?