Police said the dredging operation was "difficult and challenging".
The officer in charge, Superintendent Sue Schwalger, said the decision to dredge the ponds was made after consulting Guy family members.
"Police made the decision to dredge the ponds after it was flagged by the family and other interested parties as a potential issue. Police wanted to provide reassurance to the family and others that there was nothing of interest in the ponds."
The case remains open and police have said they will examine any new lead they receive.
"The key to any investigation is to have an open mind. As with the original investigation, police spent many hours investigating and eliminating the numerous rumours and speculation, so after further consideration of a range of views and discussions with Kylee and the Guy family police decided to take this step."
Mr Guy was shot dead in the driveway of his Feilding farm on July 8, 2010. After a nine-month investigation his brother-in-law and business partner Ewen Macdonald was charged with murder.
A jury found him not guilty of murder nearly a year ago, but he is serving a jail sentence for crimes he admitted committing against Scott and Kylee Guy and others.
In a statement, the dead man's parents, Bryan and Jo Guy, said: "The question of draining the ponds has been raised on a few occasions.
"The police had asked if they could take the opportunity to dredge the silt once the water had been drained.
"We were happy to co-operate with the request to provide an answer, and put that particular question to rest."
Developments
What have police done?
They have sifted through sludge up to 2m deep that was left at the bottom of effluent ponds on the Guy family farm.
Why have they done it?
There had been speculation that evidence could be in the sludge relating to the murder of Scott Guy. The family told police it was an issue for them and police say they wanted to reassure them.
How did they do it?
The two ponds were drained of their liquid and then silt and sludge was removed, sifted and raked through. Nothing of significance was found. The operation this month took nine days and a total of between 400 and 500 tonnes of silt and farm waste was removed.