The trio wrote "3 All Safe" on the bank of the Daly River, about 220km southwest of Darwin, on Thursday after their boat capsized in rough weather.
The men and the seven-year-old also activated their emergency beacon about 11am and the territory's police air wing unit was sent to search for the group.
It found them soon afterwards after spotting the message in the sand.
"The boaters had written a message in the sand for rescuers, indicating they were all safe," a police spokesman said on Friday.
A helicopter later rescued them and they were flown to Darwin for medical assessment and found to be well with some minor exposure.
Acting Senior Sergeant Isobel Cummins said the emergency beacon had saved the family from being stranded in "unfavourable conditions".
"This was a fantastic result and we are all very happy to see these fishos back safe and sound," she said.
The Daly River flows from its source in the hills west of Arnhem Land to its mouth at Anson Bay on the Timor Sea.
The waterway is popular for recreational fishing and regarded as one of the best places to catch Barramundi in Australia.
The NT is home to the world's largest wild crocodile population, with more than 100,000 of the predators in the wild, the NT government says.
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