Broadcaster Alan Jones and Macquarie Media have lost a defamation case brought by Toowoomba's Wagner family over deaths from the 2011 Queensland floods, with a Supreme Court judge ordering them to pay a total in $3.75 million.

Justice Peter Flanagan said the defamatory imputations published by Mr Jones on his radio shows in Sydney and Brisbane were "extremely serious and of the gravest kind", including the claims the Wagner family and their quarry was responsible for the deaths of 12 people, including two children, in the Grantham floods in early 2011.