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Using a net such as used in swimming pools is helpful for cleaning out large materials that have settled to the bottom of the pond. However, if there is a very large amount of debris in the pond you should be careful to either remove the fish or use supplemental aeration to avoid creating significant oxygen deprivation due to stirring up anaerobic or large amounts of oxygen-consuming muck.
Wet/dry shop vacs, specially those with an attachment for a garden hose to provide a continuous drain, have also been used. These devices may drain a large amount of water from the pond in a short time and therefore it is necessary to either replace the water or use the garden hose to add the water back into the pond through the biofilter.
Remain aware of any lack of oxygen for fish or other living inhabitants.