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.
