The new Water Dungeons cannot be turned off using the World Customization settings.
What I expected to happen was...
Changing "Temples" or "Dungeons" on the World Customization's Basic Settings screen to "No" would cause Water Dungeons to not be generated in the world. I was expecting to see the normal ocean terrain where the Water Dungeon was before.
What actually happened was...
The Water Dungeon still generated in the world.
How to reproduce:
Create a world and locate a Water Dungeon.
Write down your coordinates and exit the world.
Re-create the world (to get the same seed), but before creating, change the World Type to Customized and set both Temples and Dungeons to "No".
Create the new world and /tp to the coordinates you wrote down from Step 2.
The Water Dungeon will still be there.
Here were the settings I used:
Seed | 203371283943414296 |
Location | /tp 150 60 1290 0 30 |
Biome | Ocean (see note below) |
Note: I took advantage of this other setting on the Basic Settings screen to help me find a Water Dungeon. The seed and location above will not produce a Water Dungeon if you do not also change the Biome setting to "Ocean".
I was expecting that too! I thought if I set everything to no except the temples in the settings with the dungeon generator to 100 and the biome Ocean I would get tons of water dungeons... but I didn't...