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Drain the water down to concentrate the fish in the (now) deepest part of the pond. Dig the rest of the pond deeper according to your plans. Keep the pump going so you are digging in relatively dry ground vs. a soup bowl. Dig the area 1'-2' deeper than you want.
Dig a trench to let the fish and water go to the now deeper part of the pond, Now dig out the sediment/muck that is in the previous deepest part of the pond (now the shallowest part). Doing so will wash dirt/soil/muck to the now deepest part of the pond, but not more than a few feet at the most. (that's the reason for digging it deeper than you really wanted the finished pond to be).
Pray for rain to fill it back up.
While the water levels are low, put cover in the pond to help the fish population once it fills back up with water. Easier to do when on bare ground than from a boat.
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