However the man did not receive a conviction, with the magistrate saying he had already suffered "the worst thing" when his son drowned on June 6.

The five-year-old and a 28-year-old male passenger were killed after a 5.5-metre runabout hit Peggy's Reef in darkness just before 6pm.

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During a three-day hearing earlier this year the court heard the boy was wearing a flotation aid - possibly a life jacket, when a boat capsized.

Two male passengers - friends aged in their 20s - went into the open water, but the father and son went under the hard-top fishing boat into what the man described as a tight space with little air, likely in the boat's submerged nose.

"I knew I was in the cabin but I didn't know what, you know, in the water, what position we were in. So I thought ... I have to leave or, you know, both of us will die," the man told police during an interview following the incident.

The man, who cannot be named for legal reason, faced Wollongong Local Court on Thursday where he was found guilty of operating a recreational vessel negligently causing death.

Magistrate Claire Girotto said she was satisfied beyond reasonable doubt the man departed from the "standard of care" before adding it was a difficult case to determine given the tragic loss of life.

"Nothing I do is going to make anything better or worse for him," she said. "It is already worst thing.

"I do extend my condolences.

"I will not convict you because you have lost so much."

The court heard the father, from south-western Sydney, his son and two other men, had taken the borrowed boat out for an afternoon's fishing, departing Bellambi boat ramp about 2pm.

The captain had successfully avoided the reef, using a wide-arc, on the way out to sea before trying to returning to shore about 5.15pm.

Rather than using the same route, the captain returned in a straight line.

The court heard the captain used his navigational equipment on the way out but not on the way back.

It was dark, except for moonlight, and the captain said he used the lights of the carpark, to guide him safely back.

The magistrate found the man knew the reef was there, despite there being no warning devices on the reef, however there were signs on shore indicating hazards in the water.

Magistrate Girotto found the captain was travelling too quickly, at 14 knots, and may not have had enough time to react, and likely would not have heard the waves crashing on the reef.

"The impact of hitting the reef may not have been as severe if the boat was travelling slower," she said.

"He didn't use the navigation system. If he had done so then he would have avoided the reef altogether. I am satisfied he knew how to use it and had used it."

During the hearing, police prosecutor Sergeant Mark Watson told the court there were several ways the man could have avoided clipping the reef as he was familiar with the location and was an experienced boat fisherman.

Sgt Watson said the captain did not do his "homework" about the reef and failed to effectively use his onboard equipment.

The man's defence barrister Derreck Drewett said his client did not know the reef was there and therefore his actions did not amount to negligence.

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