The boat is understood to have capsized in the Durris area, at Craiglug.
The Scottish Fire and Rescue Service initially said one of the three - believed to be teenagers - made it ashore, and efforts were being made to reach the other two who were stranded on an island in the river.
They were later rescued by boat.
The alert was raised shortly after 13:45.
Three girls who sparked a rescue effort in the River Dee in Aberdeenshire after reports of a boat getting into difficulties are all safe and well.