The lake was becoming warmer at the same time in the 1800s the abundance of fish began declining, the team found. The lake's algae - fish food - also started decreasing at that time.
However, large-scale commercial fishing did not begin on Lake Tanganyika until the 1950s.
"Some people say the problem for the Lake Tanganyika fishery is 'too many fishing boats,' but our work shows the decline in fish has been going on since the 19th century," said study leader Andrew S. Cohen, a UA Distinguished Professor of Geosciences.
"We can see this decline in the numbers of fossil fish going down in parallel with the rise in water temperature."
Lake Tanganyika yields up to 200,000 tons of fish annually and provides about 60 per cent of the animal protein for the region's population, according to other investigators.
Mr Cohen and his co-authors acknowledge that overfishing is one cause of the reduction in catch. However, they suggest sustainable management of the Lake Tanganyika fishery requires taking into account the overarching problem that as the climate warms, the algae - the basis for the lake's food web - will decrease.
"The lake has huge biodiversity - hundreds of species found nowhere else," Mr Cohen said.
The warming of the lake has reduced the suitable habitat for those species by 38 per cent since the 1940s, the team found.
"The warming surface waters cause large parts of the lake's floor to lose oxygen, killing off bottom-dwelling animals such as freshwater snails," Mr Cohen said. "This decline is seen in the sediment core records and is a major problem for the conservation of Lake Tanganyika's many threatened species and unique ecosystems."
"We're showing the rising temperatures and declines in fish food are resulting in a decrease in fish production - less fish for someone to eat. It's a food security finding," Mr Cohen said.
"We know this warming is going on in other lakes," Mr Cohen said. "It has important implications for food and for ecosystems changing rapidly. We think that Lake Tanganyika is a bellwether for this process."
