In the tense final, Kunja reached the finish line in one hour, 59 minutes and 30.8 seconds.
Rio de Janeiro Olympic champion Sharon van Rouvendale of the Netherlands lost just 0.9 seconds to her, while Australian Karen Lee lost 1.7 seconds.
If Kunja was among the leaders from the beginning, then van Rouvendaal started swimming modestly, gradually accelerating his pace.
The 29-year-old Kunja made his Olympic debut in 2008 in Beijing, where he won fifth place as the youngest competitor. Five years ago in Rio de Janeiro, she was tenth.
On Thursday, men will compete in open water for a distance of ten kilometers.
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