Lack of cooperation between nations which have competing claims to the sea is also contributing to the depletion, they said.
A number of countries claim the waters, including their reefs and rocky outcrops.
A study shows the number of some species at about five percent of 1950s levels.
Several of them, such as coral groupers and Napoleon Wrasse, have declined by 80 percent in the past eight years alone, it said.
“The South China Sea is… under threat from various sources. We need to do something,” said Rashid Sumaila, director of the Fisheries Economics Research Unit of the University of British Columbia.
“The most scary thing is the level of decline we have seen over the years. Some species (are facing) technically extinction or depletion,” Sumaila, who headed the study, told a press conference in Hong Kong.
Sumaila said political disputes were also damaging fish stocks.
China claims sovereignty over almost all the South China Sea, but Vietnam, Malaysia, the Philippines, Taiwan and Brunei have competing claims in some areas.
“There are lots of peoples bordering the South China Sea… when you don’t cooperate, everybody races for the fish because the thinking is if you don’t catch the fish someone else (from another country) will catch it,” Sumaila said.
WWF Hong Kong said earlier this year a growing appetite for seafood was threatening surrounding waters, as a study showed more than half the species available in the city’s restaurant tanks were from “highly unsustainable” sources.