Hobbyman, Hydrated lime is an outstanding and fairly inexpensive solution for what you want. The least expensive method is to drain the ponds as low as you can, then use the remaining water to liquefy powdered, hydrated lime (Slaked Lime or Calcium Hydroxide used in concrete) to mix about 800 pounds H Lime per acre foot of water. Be sure to spray concentrated lime on all pool areas that may have dried also because some species of fish can live for days burying themselves in mud.
The easier method, but more expensive is to not drain and simply saturate the pond with the Hydrated Lime. This method will kill most everything and be safe to restock in 2-3 weeks.
If draining and treating, you can restock upon filling.
As Chris said, use precautions with Hydrated Lime. Dry Powder is harmless, but wet, it is very caustic and will cause some bad chemical burns on skin when prolonged wetted contact happens.
Seine, drain, and then treat with hydrated lime is exactly how I spent this last week. With only 6" of water left, less than $80 (ten bags) of hydrated lime was all that was needed to treat a drained 1/4 acre pond.
Rex mentioned fish burying themselves in the mud, so I posted this pic to show how much ground water affects this process. The reeds on the far side of this pond are at full pool. The sheen below the reeds shows the amount of moisture still leaching through the soil 7 days after this water was dropped. Every footprint, old CNBG nest, and any other low areas were given extra lime.
I don't need this pond until spring tilapia are available, so I'll let it rest until then. It's a lot of work, but much, much cheaper IF you have access to water to refill the pond after the lime treatment.
