Skunked, I had my pond muck dug out several years ago. It was originally 10 foot deep and had mucked-in to only have 2 foot of water. The water level was up at the drain, but the muck had gotten 8 foot deep leaving only 2 foot of water above it. First, the dam had a ditch cut through it with a mini-excavator to drain most of the water. Then, he came back and cut that ditch even deeper. It was too dangerous to dig the drain ditch to the proper depth to begin with as the rushing water was eroding the ditch once it started flowing out. The second dig allowed him to dig deeper than the uppermost level of the muck. This allowed the remaining standing water to escape and allowed the water saturated muck to mostly de-water and run out. The pond was left like this for several months and the muck turned from a total soupy mess to having a dry and cracked surface that was 12-18 thick with damp muck beneath it. A track loader was used to remove the muck. He started at the edges and got down to the original clay bottom. This gave the tracks something to bite into as he worked into and out of the pond with the muck. Once the pond was dug out, the breech was back filled a layer at a time with good clay.
Some have had success by using pumps, but my pond gets way too much watershed and needed the breech in the dam to allow that run-off to continually run out and not over take the pumps and fill the pond back up.
The above is a good approach, but keep in mind that I did not make my pond deeper than it was originally. If you decide to go deeper than original, you will have to evaluate the clay content as you dig. If you break into gravel or sandy veins or rock shelves...you may have to layer good clay back in once the desired depth is achieved.
I have to ask where most of the water went? If the pond is leaking currently...that's something you'll have to address as well.
