Biologists in Singapore were puzzled by the turtle's behaviour because, despite using its lungs to breathe air, it often submerges its head in water.
By testing the water, they found that the reptile was excreting urea through its mouth instead of its kidneys, the BBC Nature reported.
The discovery adds to previous research, which suggested the turtles have highly specialised mouth tissues.
The species, Pelodiscus sinensis, is found in swampy, brackish water and is native to much of East Asia.
Observations of the species noted that they occasionally submerge their heads into pools of water for up to 100 minutes.
Professor Ip Yeung Kwon and colleagues from the National University of Singapore brought a turtle into the lab to study how the turtles did not drown and to observe what else may be happening.
Researchers provided the turtle with water and observed as it regularly dipped its head and rinsed water through its mouth.
The turtle's rhythmic motion of its throat, not to mention its survival, signalled that it was indeed breathing during these submerged spells.
Scientists also analysed how the chemistry of the water changed after the turtle interacted with it and found increased levels of the chemical compound urea.
The majority of vertebrates expel urea, a waste product full of nitrogen, through urine via the kidneys.
In turtles urea passes out of the cloaca - the single orifice used for waste matter and reproduction.
"Throughout [the study] period, the urea excretion rate through the mouth was significantly greater, 15- to 49-fold, than that through the cloaca," said Ip.
Ip told BBC Nature that the ability to pass waste through the mouth was unique to this species but suggested that the ability could be evolutionarily linked to how some mammals such as bats, cattle and goats "recycle" nitrogen by excreting urea through their saliva.
"We were greatly surprised by our novel results because it is generally accepted that the kidney is responsible for the excretion of urea in vertebrates - except fish," he said.
The study was published in the Journal of Experimental Biology.
