However, despite earlier reports, the dive did not set a new record for a freshwater descent.
Scientists plan to collect samples at different depths and hope to document the effects of global warming on the lake, and draw the attention of the government to the need for greater environmental protection.
The scientific expedition was organised by Artur Chilingarov, a pro-Kremlin member of parliament and an Arctic explorer who led the submarine team that planted the Russian flag at the bottom of the North Pole last August.
"We want to study and observe Baikal, preserve it," Chilingarov said on Monday, ahead of the dive as he inspected the Soviet-designed Mir-1 and Mir-2 submarines in the small port of Turka on the shores of the lake.
Anatoly Sagalevich, an expedition member, said the mission could find new species of wildlife living at the bottom of the lake, which has never been explored, as well as possible reserves of oil and gas.
Chilingarov said the expedition had "full support" from Vladimir Putin, Russia's prime minister.
Environmental groups say pollution is threatening the pristine lake.