He claimed to have blacked out after a coughing fit, waking when the car was in the water. He later said he tried to save the children but failed. Jai, 10, Tyler, 7, and Bailey, 2, drowned.
But on Friday the Supreme Court jury of five men and seven women held him guilty on three counts of murder after deliberating for almost three days.
Farquharson blanched as the verdicts were announced. He raised his eyebrows and shook his head from side to side as if in disbelief.
Justice Cummins remanded Farquharson for pre-sentence submissions on a date to be fixed. He said he hoped the case could be concluded promptly, possibly by the end of the month.
Outside court, Farquharson's solicitor seemed shaken. Senior defence counsel Peter Morrissey told reporters as he left the court building that he had already received instructions to appeal.
"The jury found Robert guilty, but I can tell you he maintains his innocence of the charges. He will maintain his innocence in court during the plea," Mr Morrissey said. In interviews with police, Farquharson had denied having deliberately driven into the dam.
"I'd do anything to have them back, and I've got to live with this for the rest of my life, that I couldn't save my kids," he said.
But the senior prosecutor, Jeremy Rapke, QC, said there was powerful and compelling evidence against him, including Farquharson's long-term depression, his anger over the break-up with his wife Cindy Gambino, evidence about the path of the car, and Farquharson's alleged coughing fit.
One of Farquharson's friends, Winchelsea bus driver Gregory King, testified that Farquharson had told him outside a fish and chip shop that he would kill his sons in an accident — which he would survive — on a special day, like Father's Day.
Mr King said Farquharson told him he would take away the children, the most important thing for Cindy Gambino.
He said Farquharson added: "Something like Father's Day, so everyone would remember it. When it was Father's Day, and I was the last one to have them for the last time. Not her."