It sounds to me like you have a leak and muck problem. You also may have had some runoff into the pond with fertilizer? Has anyone fertilized nearby where it can get in the pond?
It does depend on your goals and what you are willing to spend. If it were me, I would first try to measure the muck depth to get a gauge of how juch effort to clean the pond out would be. If under a couple of feet, maybe some aeration would help reduce the muck. If over that, there may be too much accumulated nutrients to too shallow of water to do anything much but clean it out. There are some treatments available to lock up nutrients in the pond to keep it out of the water column.
If you decide the pricy route of a clean out, you may be able to address leaks at the same time by bringing in some clay to line the pond after cleaning. Perhaps even finding clay somewhere on site would be good.
If you do suspect a leak, but cannot go the lining rout, you can re-core the dam which is also expensive, and may not fix the leak. However if it is muskrat damage through the dam, this would fix it, and you would be able to keep existing fish.
