Muck is ok in natural wildlife ponds but in ponds containing fish, it can lower oxygen levels and encourage algae growth. A lined fish pond shouldn’t have any detritus on the bottom, dealt with by a combination of filtration and maintenance.
And if the pond is unfiltered the muck will have to come out before the pump and filter go in, as otherwise, they will just block within hours.
Net it out
If the bottom material is made up of leaves, fruits, or nuts you may be able to net it out. Use a coarse net with a strong handle and draw it across the base of the pond until its clear.
If small particles are left behind in the water draw a finer net through the midwater, removing as much as you can.
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