Here is a technique that I tried and it worked perfectly. I was kayaking on a large body of water, secluded on all sides by tall bulrush plants and only a foot or less of water on top of a thick under-layer of fabulous mud. I wanted to play in that mud, but without the water being on top. So I made it happen and here is how you can do the same thing.
I chose a spot to create my mud area and went outside of this area and dug the mud from the bottom and built a sort of dyke or wall in the shape of a large rectangle. The pond now had a rectangular pool of pond water surrounded by a dyke. The mud was still beneath a foot of water inside of the enclosed area.
So next, I took my kayak paddle and used it as a shovel, scooping out more of the mud below and tossing it into the middle of the enclosed area. Eventually, the enclosed area filled deeper and deeper with mud, causing the surface water to overflow the dyke. After about half an hour, I had raised the level of mud inside the enclosed area enough that all of the surface water had been replaced with the mud. Viola! A nice rectangular area of mud sitting in a large pond.
I had to be careful not to disturb the edge of the area, but I was able to get into the middle of the mud rectangle and it was amazing mud. Of course rinsing off was easy, because I was already in a large pond, so I just had to clean up and get back in my kayak.
So if anyone discovers a similar situation where mud is under some water, this is a technique where you can create a mud pit which is level with the pond.
In the photo, you can see the enclosed area ready to be filled with the bottom soft mud.
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Second scenario: The mud is too shallow. Simply dig a deeper area and fill it with surface mud until it becomes a deeper mud pit. The photo shows an area of water where soft mud was removed to fill in the mud pit in the foreground.