The man and woman, who were both in their seventies, were found unconscious in shallow water at Michaelmas Cay, a popular tourist spot about 40km (25 miles) north-east of Cairns.
Their bodies were discovered at around 11:00 local time on Wednesday (November 16), police said.
They were among a group of 21 French holidaymakers visiting the reef with Australian tour operator Passions of Paradise.
The couple are believed to have suffered cardiac arrests, Brisbane-based newspaper The Courier-Mail reports.
"The two people indicated they had pre-existing medical conditions before they got in the water," Col McKenzie, chief of the Association of Marine Park Tourism Operators, told BBC News.
"The company actually had guides in the water swimming around the snorkellers making sure they were OK."
According to McKenzie, the man was spotted in distress first and was pulled from the water by a lifeguard, who attempted to resuscitate him on the beach.
The woman was discovered shortly afterward.
"Minutes afterward, the lookout who was working on the boat spotted somebody face down in the water, not moving. They swam over and pulled them onto the boat and commenced resuscitation,” he explained.
McKenzie added that Passions of Paradise had taken more than 400,000 people to the reef since it began operating in 1989.
Scotty Garden, chief executive of Passions of Paradise offered his sympathy to the pair’s family and friends and said the operator would offer assistance to travellers who needed it.
"It is very stressful for our staff but their priority has been with helping the group," he said in a statement.
