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It may be my inner OCD, but situations like this annoy me to no end. Sometimes, a patch of water is "ruined" for no apparent rational reason and all attempts to restore it to normality are met with failure.
My latest attempt was building dirt where the currents were, then removing it. The result is pictured. :/
Is there something I can do about it, or is it just a glitch?
Place dirt right underneath the crazy currents and it should sort itself out automatically.
If it doesn't, add a source block to the place all the water flows to.
The problem is that there are missing source blocks (aka spring blocks) from the top level of the lake.
Since water source blocks only replicate if there is a empty block that is adjacent to two source blocks and has a normal block underneath it (no glass, reeds, mob spawners or anything like that.) it can't refill the top layer of a deep lake. One way to fix it is to make it a shallow lake by placing dirt under it, but this can lead to underwater currents when the block is removed.
The cleanest way to fix it is to re-fill that missing source block with a bucket. But you say there is no solid block to pour the bucket out on to? Then place a block above it!.
And dive under it, look up and dump a bucket of water.
No underwater currents created!
Of course, in my example pictures, it's only 2 blocks deep, so a dirt block on the bottom of the lake would have worked just as well.
There's a new solution to this that requires Creative mode in multiplayer, and even works underwater.
First, go into creative mode fill the affected area with ice blocks. You can enable Creative in multiplayer by typing /gamemode <username> creative in chat.
Next, go back into Survival mode (/gamemode <username> survival) and smash them with a pickaxe.
Ta-da! The smashed ice blocks are now water source.
In version 1.5 (and beyond), this issue of non-source blocks mussing up your lakes can only occur if you lake has missing source blocks (flowing water) all the way to the bottom of the lake. this can drown your animals, so there is more reason than ever to repair it.
To fix it, place blocks on the bottom of the lake under any flowing water. This will recreate and update all the rest of the water all the way to the surface. if this doesn't fix everything, place another layer. Large areas of flowing water (from supercharged creeper blasts or improperly made artificial lakes) may require placing a bucket of water or two on the blocks you have placed.
When it is fixed, you may remove all the blocks you have placed.
I've had trouble with this as well. My solution was to wall off my pool into 4-by-4 (1 deep) cells and fill those with water using the "endless well" technique of emptying a water bucket into two opposite corners.
Once you've filled every cell, you can start breaking down the walls between the cells one block at a time. Sometimes the same effect that makes the endless well work will fill the removed block fully. Sometimes it won't. If it doesn't, empty a bucket directly onto the space.
For pools more than one block deep, completely fill the bottom layer and then build the cell network for the next higher level "suspended" over your filled layer and continue the process.
Repeat ad infinitum. Obviously this takes a lot of time and effort.
Of course in your case, since you just have one "little" problem area (compared to the total area of your pool), try walling off just that area, removing the water, and trying my method above, destroying the outer walls last.
The key is to remember that water in a bucket is a block just like everything else.
I've created a mod that fixes this problem. It's available here.
Under the block that is "oddly" flowing, place a block under it it works for me.
Here is a suggestion: if you have ice blocks, place them where the crazy currents are and break them. If you have no ice, then you will need a bucket of water, an infinite water source and some scaffolding. Like with the ice, place your scaffolding over all the currents, except one. Empty your bucket there. Refill the bucket using your infinite water source. Then break another scaffold and empty your bucket there. Rinse and repeat.
