It sounds like the pond is in need of major work. Un-decomposed organic matter mixed in with soil underwater is going to be food for anaerobic organisms and the products of such metabolism includes methane along with other things that displace oxygen and can be toxic. Cleaning an old pond presents technical problems that can make it a bigger challenge than digging a new pond. Small draglines are fine, but a clam on a small crane is great if you have lots of slop and the stuff just fills in where you pulled the bucket out. I know a thing or two about using both. The dragline is best when the material has enough body to it that it feeds into the bucket and stays in the bucket. Of course, where is this machine going to sit and where is the material going to go when it does its thing? Clams might be better is some cases, but not many know much about them. They don't stir things around as much. The long reach backhoes today have replaced the small draglines of a cubic yard or less and more people today can get a job done with them. A friend of mine leaves his 305 Koehring parked and uses his JD 240 long reach for doing small retention ponds these days. The person doing the job may use a combination of draining part way and various digging strategies. Hire someone who knows how to do this work. Be mindful that when times are tough, a contractor will take any job even though they may not have the best equipment or experience to do it and make a big mes$. A mediocre dragline operator is also going to waste time.

Enough said about the equipment. If you get this thing cleaned out, you may want to consider building a trap where the water flows in so that the kind of excavator that any contractor would have can reach what is in there and you can keep it cleaned out routinely so less silt enters your pond. You also might want to have an arborist look at the trees around the pond to see which ones are really worth keeping. You don’t want the leaves in there and too much shade is not good. Removing a few trees if the cattle have not already done so will do a number of things. First, it will give the contractor more options in which they can perform mechanical removal of material. Second, having more light will increase photosynthesis which is the base of a food chain in most ecosystems and provides oxygen. Of course there are a number of issues involved in this. Having the right kind of vegetation and not just a weed and/or algae problem is a concern. The fertility of the pond bottom to support desirable aquatic vegetation should be taken into account. You may have to buy some aquatic plants to get things started. I don’t know what the fish are supposed to do during such mayhem or what you want to spend, but these are just some thoughts.