Water is a bit of a tricky beast..
Generally water that is only one deep will self level. So if you want to level out water, build a layer 1 block beneath, it will level and you can then remove that layer. There is another way but it is a bit difficult to explain, better to show you in game if you need it.
One thing to be wary of though is that doing anything underwater will create currents if you're not careful, and if you get stuck in a current, it is very easy to drown because it is difficult to get out.
Currents form underwater when you remove blocks. But if you remove blocks from the top down, you don't get currents, because the water can level itself.