What I would do is give myself ice blocks, fill up the lake, and then break the ice blocks.
That's the easiest way, in my opinion.
gaming.stackexchange.com/users/12553/gamewin1
There's no practical way of fixing this ingame.
The closest would be to fill in the area completely with sand, then systematically replacing each block with a water source from a bucket area, column by column
(you can't do this layer by layer without having nasty downwards currents ).
If you don't want to use external programs, I suggest claiming this area entirely to your base.
Make it a small and cozy underwater base or something (making a layer of water deep 1 is still a lot of work, but one level of magnitude less than clearing that mess.)
If you do want to use extenal editors, tools like Worldedit have what you need ( /fixwater ).
gaming.stackexchange.com/users/23/badp
I've a technique that I've used to fill in some large lakes; as well as a deep and wide network of canals and moats.
It requires some patience though.
Here's the solution I use to fill in large bodies of water: You will need: A couple of buckets; At least two, but more if you don't have a convenient way to replenish them.
Lots of easy to destroy blocks.
I usually use cloth because it can be broken quickly and stands out well against natural blocks, but dirt works just as well.
Needless to say, you cannot use sand or gravel because it is affected by gravity.
Make sure the area to be filled is initially dry so that you can make sure you fill it completely with spring blocks.
Starting from the very lowest layer, place spring blocks until the bottom layer is fully flooded.
Fill the next layer with your cloth blocks * ;
Every empty space that must be filled with water needs a cloth block instead.
Starting from the center of the area to be filled, remove blocks one at a time and put a water spring block in its place by targeting the edge of the adjacent cloth block.
Once the current layer is completely replaced with water, go back to 4.
*
You can actually optimize this a bit by placing the blocks in stripes spaced two apart.
Filling first the spaces, and then going from one end of the stripe to the other, removing each block and replacing it with water.
gaming.stackexchange.com/users/2798/SingleNegationElimination
It looks like the section of lake here forms the corner of a rectangle, yes?
Like so: Assuming O is 'correct' water, and X is uneven water:OOOOOOOOOOOOOOO XXOOOOOOOOOOOOO XXXXXOOOOOOOOOO XXXXXXOOOXOOOOO XXXXXXOOXXOOOOO XXXXXXOOXXXXOOO XXXXXXXOXXXXXOO XXXXXXXXXXXXXXO XXXXXXXXXXXXXXO
In that case, this should be relatively easy: just cover the entire corner in dirt blocks, each placed one block beneath the surface of the water.
Once the entire corner is covered, the water level will flatten, and you can destroy the dirt blocks to fill in the bottom of the lake.
The only reason you should need a water bucket is if there's an entire horizontal or vertical row of blocks that's uneven.
gaming.stackexchange.com/users/11689/jsnlxndrlv
First, fill it up with sand or something up to the water level.
Then pour water all on top.
After this dig out the sand until you get the level you wanted.
gaming.stackexchange.com/users/7468/Not a Name
water creates a source block when the following happenX=Source waterO=created source water XO OX XOX
If you refill the uneven part, grab a water bucket and use the above to place minimum water it will flatten out
gaming.stackexchange.com/users/104531/Namiknight
I have a pretty big job on my hands here.  I've dug out a lake, problem being it's not flat anymore.  Would be best idea/method to solve a water problem on this scale!?
How do I sort out this mess of a lake?
gaming.stackexchange.com
<minecraft-java-edition>
gaming.stackexchange.com/questions/30663
gaming.stackexchange.com/users/4528/wonea
You can fill up the lake with easy to destroy blocks, like ice blocks, then destroy them.  It is proposed that straightforward in-game actions or external tools could be a solution.
It is suggested that certain in-game techniques involving ice or sand blocks could flatten the water. External tools could be an option in order to flat the water.