Big Blue was thought to have been a relic Plesiosaur, and the only time it was seen (albeit briefly, in poor lighting and with the bulk of it's body submerged) it did appear to have a long neck and small head.
The animal was believed by Agent Mulder to have been responsible for a series of gruesome murders around a lake in Blue Ridge, Georgia. As things turned out, the deaths were caused by an anomalous alligator which was loose in the area. At the end of the episode, Big Blue was living happily, still undiscovered in the lake.
The Blue Ridge locals had built up something of a tourism business based on the legend of Big Blue, much like the locals of Loch Ness have done with Nessie, although Agent Scully notes that most of the so-called "evidence" is most likely fake.