The grey and white mammal became stuck on sandbanks on Thursday at Saltney Ferry, near Chester.
An RNLI lifeboat hoisted the dolphin out of the water before carrying it out to sea, according to the British Divers Marine Life Rescue.
The dolphin, in the river since Monday, will be taken three miles off the coast of Rhyl.
Alan Forrester, lifeboat operations manager with Flint RNLI, told Radio Wales the rescue boat was launched at Connah's Quay after the dolphin was seen "floundering" on a sandbank.
It was hoisted onto the lifeboat and carried down the river towards open water.
An animal welfare officer is also onboard.
"We've got what we call an ambulance pouch, which is a rolled up stretcher," Mr Forrester added.
"They laid that on the sandbank and rolled the dolphin into the stretcher and lifted it into the lifeboat.
"It's rather a large dolphin. It's lying there nicely, they've got buckets of water to keep it cool - everything seems to be ok at the moment."
The mammal was originally spotted by the public on Monday in Connah's Quay docks and became stranded briefly on Tuesday after turning to make its way to Flint and towards the sea.
Liverpool coastguard wanted to hold off a rescue attempt for as long as possible to avoid coming into physical contact with the mammal in case it is rejected back at sea.
A coastguard team was earlier deployed to the area to try to ensure the safety of spectators trying to catch a glimpse of the dolphin.
It is thought the dolphin swam up the river during the high spring tide.
It is rare for dolphins to be seen in the River Dee but a pair of porpoises were reported near  Queensferry Bridge eight years ago.
A dolphin has been rescued after swimming miles up the River Dee in Flintshire four days ago.