So you wanna make an underwater base?
Well, it just so happens I am the MASTER at making underwater base :D Not to brag! I just want to lift up your spirits about this whole underwater base thing!

Some things you should know:

If you don't choose your method carefully, there could be some difficulties. Ex: One base may be better for a multiplayer game than for a single player, and one may be better for a single player game than in multiplayer.

You may have to/should modify these techniques to fit your faction's/group's/partie's/town's needs.

If you need to substitute a block, just be careful what block you are substituting. Some make better substitutes than others.

So, let's get started!

METHOD ONE YAH

For method one, you will need a steady supply of glass, diamond and iron pickaxes, and torches.
Firstly, you will need to find a find an island(at least 2000+ or further blocks away from spawn if on a pvp server) that is big or small enough to build your base. It must be flat, this picture should be a good example:



So yea thats a big picture. Sorry bout that. Anyway, it should be NO BIGGER than that, and if you are limited on tools, go small. The bigger, the harder it is to make, and the longer it takes.

Dig a hole, like turn the whole island into a hole. Just don't dig the blocks that are keeping the base from being submerged, because we are going to submerge it later, but only when the base is ready.

Your hole should be pretty deep. Now, once it's finished, make the ceiling out of glass. Make sure the glass is one block BELOW where the water would be so when we can have it totally submerged. You may want to go up below the base to make sure everything is going good.
Once this is done, and the ceiling is finished, make a hole next to where the ceiling is and use it as a way to get down into the base(and make go down to a block below where the floor is so instead of getting water all over the place, it'll be a nice orderly stream.

Then, it's all up to you to decorate!

METHOD TWO YAH

You need to find a shoreline for this one, now this is mainly for factions and you should be REALLY REALLY SUPER FAR AWAY from spawn to do this one. Like a place of the map where nobody has ever stepped food before, m'kay?
Now this is going to be both in the sky AND underwater. I may upload a tutorial on skybases themselves, and skyspawns are very safe for factions as long as there is no way to get to them and only a safe way down.

Now you wanna set home on the top of a tower of the chosen block(I do not recommend wood), and it must be far up enough that when you jump off you die.
So start building a room from the top and leave a two-by-two hole you are going to use to get down.
Now dig a hole directly under the base, matching up with the two-by-two hole so you can put either a stream or ladders to get down and it won't leave a great big mess. Now go very deep down(make sure you still have your home set up above) and once you think you are at a good spot, make your "underwater" room. Well, it's more underground, but you should put "windows" with water behind them so people will think it's underwater.

There are some other methods, and I'm eager to share them, but that has to be all for this tutorial. Bye!