Africa's Lake Tanganyika has heated up sharply over the past 90 years and is now warmer than at any time for at least 1,500 years, a scientific paper said on Sunday, adding that fish and wildlife are threatened.

The lake, which straddles the border between Tanzania in East Africa and the Democratic Republic of the Congo, is the world's second largest by volume and its second deepest, the paper says.

The lead scientist on the project, Jessica Tierney, said the sharp rise in temperature coincided with increases in emissions of greenhouse gases seen in the past century, adding to evidence that emissions are warming the planet.

The 'Great Lakes' such as Tanganyika, Malawi and Kenya's lake Turkana were formed millions of years ago by the tectonic plate movements that created Africa's Great Rift Valley.

Some 10 million people live around Tanganyika and depend upon it for drinking water and food, mostly fish.

Geologists at Rhode Island's Brown University used carbon dating to measure the age of sediment on the lake floor. They then tested fossilised micro-organisms whose membranes differ at various temperatures to gauge how hot it was at times past.

The results were published in Nature Geoscience on Sunday.

"Lake Tanganyika has experienced unprecedented warming in the last century," a press release accompanying the paper said. "The warming likely is affecting valuable fish stocks upon which millions of people depend."

Most climate change studies have focused on the atmosphere, but increasingly scientists are studying the effects on the oceans, seas and lakes, which all absorb a huge amount of heat.

The paper argues that recent increases in temperature are correlated with a loss of biological productivity in the lake, suggesting higher temperatures may be killing life.

"Lake Tanganyika has become warmer, increasingly stratified and less productive over the past 90 years," the paper says.

The rise in temperature over the past 90 years was about 0.9 degrees Celsius and was accompanied by a drop in algae volumes.

"We're showing that the trend of warming that we've seen is also affecting these remote places in the tropics in a very severe way," Tierney said by telephone from the United States. "We've seen intense warming in recent times ... not (due) to natural variations in climate."

She said marine life had been harmed because in a lake as deep as Tanganyika, the nutrients form at the bottom but the algae needed to make use of them live at the top.

Higher surface temperatures mean less mixing of waters at the top and bottom. "That's why a warmer lake means less life."

But the paper admits that other factors, like overfishing, may be doing more harm than warming.