He was taken by helicopter to hospital in Coyhaique but had stopped breathing when he arrived, doctors said.
Mr Tompkins bought up large tracts of land in Chilean and Argentine Patagonia to keep them pristine.
A military patrol boat rescued three of the kayakers on General Carrera Lake and a helicopter lifted out the other three, the Chilean army said.
"Doug was a passionate advocate for the environment," said The North Face in a statement. "His legacy of conservation will help ensure that there are outdoor spaces to be explored for generations to come."
On his Chilean land, Mr Tompkins created Pumalin Park, 2,900 sq km (1,120 sq miles) of forest, lakes and fjords stretching from the Andes to the Pacific.
He also became involved in local environmental issues in Chile and Argentina and helped raise environmental awareness there.
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