The operation to dredge the ponds has been completed in the past fortnight, the Herald can reveal - but has found nothing of significance.
Police spent nine days sifting through 400-500 tonnes of mud and silt - something many people, including Mr Guy's widow Kylee, have been wanting to see happen - after family members said it was an "issue'' for them.
The search has confirmed a long-held police view that no evidence relating to the murder would be found in the ponds - and will be a blow to those who hoped they would provide fresh clues as to who killed Scott Guy.
There has been speculation that the murder weapon or other items relating to the investigation could have been hidden in the ponds, that were not dredged during the nine-month murder inquiry.
Mr Guy was gunned down on his driveway on July 8 2010. After a high-profile investigation police charged his brother-in-law Ewen Macdonald with the murder, alleging he was motivated by a fear of losing his place on the family farm after years of tension and feuding.
Macdonald was acquitted of the murder by a High Court jury almost a year ago. He is serving a jail sentence for crimes he admitted committing against Scott and Kylee Guy but has always maintained he did not kill him.
Superintendent Sue Schwalger, who led the murder investigation, said today no new information led to police deciding to dredge the ponds.
Only cattle ear tags and farm rubbish were found.
"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.''
She said the dredging would provide further reassurance to the family and public the police investigation was thorough. The file would remain open and police wanted to hear from anyone who had any information on the case.
Police said they have maintained close contact with the family since the trial ended and dredging the ponds had been discussed a number of times.
"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.''
Ms Schwalger said the dredging took place alongside routine maintenance on the farm.
In a statement, Scott's parents Bryan and Jo 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.''
The couple said they would never forget Scott but had to rebuild their lives and adjust to a ``new normal``, for them, their children and grandchildren.
Private investigators hired by Kylee Guy earlier this year argued for the ponds to be emptied because they believed there was a chance they could contain key evidence.
Private investigator Mike Crawford and his team were asked by Mrs Guy and the Sensible Sentencing Trust to find out who killed her husband.
Crawford told the Herald on Sunday sludge in the two ponds could hold the key to the case.
"I can't think for the life of me why they weren't drained, then completely emptied out,'' he said.
Crawford said he was told police were reluctant to properly search the ponds as they believed evidence could be destroyed as it was pulled up through suction machinery.
But Crawford said a South Island dredging company had told him that was "complete rubbish''.
"You put grilles and nets and stuff over the end so nothing actually gets sucked into the machine,'' Crawford said. "I don't want to be openly critical but it's something the police need to address. There is a metre of sludge on the bottom of those ponds which has not been searched.''
Crawford said Kylee told him: "The police have got to do it.''
- By Andrew Koubaridis of the New Zealand Herald
