The rest of the Stronghold might exist but the portal room may have become detached from it, so other parts of the stronghold may be in the vicinity, just unconnected.
Then again, it might not. From what I understand, aside from the portal room (which always generates intact), the rest of the stronghold can only replace existing dirt or stone, so if it "tries" to generate in water, it just won't generate at all.
There's a good chance the rest of the stronghold is actually there. What's the seed for this world? It'd be nice to see it and explore the other bit. Does anyone remember the 'Dossier' seed where a stronghold was in the ocean at the spawn? Well, the rest of it was there. Only portal rooms will spawn in water as they're vital for the journey to the end. However, the portal can be intersected by mineshafts breaking through it.
Seed is 2598705647906425056. The coords of the stronghold are X: 27 Z:805.
This brings up an interesting point (with me, anyway). Now that I've found one stronghold and defeated the enderdragon, why bother seeking out the other two? What is the benefit of finding another portal? The loot in the dungeon (saddles, etc., that can't be found elsewhere)? The sheer pleasure of exploration? What, what?