The 37-year-old, who partnered Tim Baillie to an historic first GB canoe slalom gold at London 2012, began competing in the early 2000s and also has a European Championship gold medal.
He was awarded an MBE in 2013 for his services to the sport.
"It is time for me to announce the end of a huge chapter in my life," said Stott.
"I consider myself both extraordinarily fortunate to have reached this point, and to have the full array of choices before me to take my life forward.
"Although I have won an Olympic gold medal at a home Olympics, I am sincere when I say that I value my journey in canoe slalom so much more."
The highlight of Stott's career came at London 2012 when he and Baillie claimed gold, a year after he had dislocated his shoulder.
Baillie retired in 2013 and Manchester-born Stott and his new partner failed to qualify for the 2016 Olympics. Team GB's place in the men's C2 was taken by David Florence and Richard Hounslow, who would go on to take silver in Rio.
Stott has suggested he will continue in the sport in some capacity, saying: "My ambition is to help more people realise their potential, so I want to build on my knowledge gained during my career."
British Canoeing's performance director John Anderson said: "Etienne has been a wonderful athlete and ambassador and we thank him for all he has done for our sport in the UK.
"We wish Etienne and his wife Georgie every success and happiness in the future."
British Olympic gold medal-winning canoeist Etienne Stott has announced his retirement from the sport.