Jones began his attack on the Wagners on 2GB in October 2014 when he claimed a high-level cover-up of their involvement in the deaths.
He took to the airwaves about 30 times to discuss the matter before relenting in August 2015.
Justice Flanagan noted the effect the comments had had on the Wagners.
"Prior to the publication of the defamatory broadcasts, each plaintiff enjoyed an excellent reputation for honesty and integrity, both in business and community circles," he wrote.
"The publication of the defamatory broadcasts was very extensive.
"The defamatory broadcasts have caused each of the plaintiffs to suffer profound personal hurt and harm to their reputations, which includes their business reputations."
Toowoomba brothers John, Denis, Neill and Joe Wagner had sought $1.2 million each from the three defendants plus veteran journalist Nick Cater, who had the complaint against him dismissed.
The $3.7 million in damages smashes the previous record Australian defamation payout when Perth barrister Lloyd Rayney was last year awarded $2.62 million after police defamed him by naming him as the "prime" and "only" suspect in the murder of his wife, Corryn.
Justice Flanagan noted an independent inquiry into the floods by Walter Sofronoff QC had found the deaths would have occurred from the sudden surge of water into Grantham irrespective of the quarry.
Justice Flanagan also deemed defamatory the claim the Wagners had put their interests ahead of the nation's by "illegally" building their Wellcamp Airport in Toowoomba and were able to do so due to political access.
Denis Wagner says he does not expect an apology from Jones.
"Mr Jones and his co-defendants relentlessly misled their listeners and the people who had trusted them to be honest and truthful," he said outside court.
"We decided to take a stand against this abhorrent, vicious, deceitful, spiteful behaviour.
"Justice Flanagan has delivered a judgment today which has clearly indicated that people, regardless of how much influence they may consider they have, will be held accountable for their words and actions."
"All we required from Nick Cater was an apology. That was not forthcoming, hence the reason he has included him in the action," Denis Wagner said.
"We will consider our options on that going forward."