Hey there Koi4JT! I appreciate your comments, the check valve was something I had not thought of and makes total sense, it is those little things that when forgotten can create a terrible mess. Thank you. I have a couple updates and a couple more questions which have arisen.
Following some other people's suggestions I began posting and communicating with people on mud pond forums and fishing lake forums. There are very few people who have tried and have been successful with keeping a earthenbottom pond clear. In fact, as Meyer Jordan pointed out to begin with, it is impossible without being prohibitively expensive. The one recommendation I received was to build my bog on top of a network of milk crates or something similar and install a bottom drain to flush it out, a process similar to what you have suggested. Apparently this was done on a much larger scale and worked to some degree. My thought process was maybe build a raised a portion, like a box or cage, on the deepest end of the bog with an opening on top where I could drop in a pump to remove the sludge as I flush it out from the other side. It wouldn't be too difficult to build, I have lots of scrap metal, but I am not sure if that even makes sense or is necessary. Other people have dug separate ponds, as big as my whole system, just to use as a massive bio/media filter. In my mind, the "bog" I am constructing would work in a similar, likely less effective, way.
Reading about the safety of swimming holes and microbial growth is a disenchanting exercise and I recommend it to absolutely nobody. I am fully aware of the risks of bodies of water and will do my best to provide a safe environment for myself and others but there is danger everywhere. I can only accomplish so much with the resources I have available and fail to see the logic in spending an inordinate amount of time and money on keeping a "natural" body of water sterile. As far as chlorinating the pond I do not think that is an option for me. Our family group that lives on the property absolutely prohibits the use of bleach, caustic chemicals, pesticides, etc. They are very, very, environmentally conscience. (For example, I live in a separate house and they get upset if I use bleach to wash my sidewalks because it "kills the plants and gets in the aquifer". You have to love old hippies but you cannot always reason with them.) I spoke with a fellow who may be able to help me procure a UV clarifier in the long term but I have no plan until then. In addition, to actually sterilize a pond this size with UV would cost 1000's. I have to do more research to see if a smaller UV sterilizer on a pond this size would do any good at all or just waste electricity. If that plan does not work than I will have to hope that aeration and the introduction of good bacteria will be enough to keep the body of water relatively safe.
I have been searching for cheaper alternatives to lining the pond and constructing a filtering system and have accumulated quite the hodge podge of things to use. I have some liner scraps from previous projects and some my neighbor was planning on using but doesn't have a use for now, 300 lbs of bentonite clay, a large stack of cinder blocks I forgot I had on a pallet in the woods, and a pile of leftover cypress boards from a deck we built. The plan is to drain the pond, pack down the clay, seal the edges where it may leak with the bentonite clay. Because the hole holds water would it be completely insane to use the liner I have to line the pond in overlapping portions solely to minimize the amount of debris that is kicked up? I believe I already have a good solid basin, I do not think I need the liner to hold the water in. The idea is to drape the liners over the sides, tuck them in or under the berm, and then lay a liner on the bottom. I could use the random cinder blocks to construct a ring around the base which would prevent the liner from floating up at all. I am open to criticism and fresh ideas. I cannot afford a full liner at the moment and waiting on funds would delay the project for an extended period.
I filled the pond to maximum capacity overnight (accidentally on purpose) and monitored the water as it drained out to find leaks and measure overall drop over the course of a hot week. For reference the pond has 2 foot tall "berms" circling the entire hole. I don't know if you can tell by looking at those pictures but the ground level is where the layer of dirt is when you look at the striation, the mounds above that is just the clay that I haven't been able to move around. The water filled and was overflowing the lowest edge of the mounds, it was pretty scary actually, I thought all those layers where you can see it already eroding away would erode further and cause the "berms" to cave in with it.
The water drained out under the berms, where the excavated clay just sits on the topsoil, but stayed steady after that for a week. So, the soil ring at the top is either super saturated or only allowing small seepage which works for me. The water settled out and was a nice clear green color until I entered the pond and would become that murky grey once again.
I dont have many days to work with and didnt want a giant stagnant water hole while I wait for my time off so I drained the pond yesterday. To nobody's surprise there has been significant erosion on the two walls visible in the picture above and a nice thick (foot deep if not more) layer of mud that is now sitting at the bottom of my project hole. To prevent more erosion I though about sinking cypress logs vertically at each corner of the hole and then laying cypress boards behind them to form a barrier. I could also just allow the erosion to continue until it forms a more natural slope and then lay the liner over that after I pack it down.
Please keep in mind I cannot keep this hole dry, there is a continual ground seep from two spots that feed this pond. In order to get the pond free of muck so I can line it I need to continually pump out the water and shovel out the mud. OR I am going to rent a diaphragm pump and let the machine do the heavy lifting when I have weekend off.
Lots of fun in the mud for me to come. Again, all criticism, skepticism, and input is appreciated! Thank you all for your help.