Scientists on board planned to take samples of water and soil from the lake, which is home to more than 1,700 unique species of plants and animals, including a species of freshwater seal. They also were to plant a Russian flag in the lake bed.
Ecologists worry that factories, a uranium enrichment facility, timber harvesting and climate change are threatening to destroy the natural haven that attracts scholars and tourists from around the world.
Television pictures showed the two brightly painted submarines disappearing into the glistening turquoise waters.
They reached a maximum depth of 5,223 feet in just over an hour, according to Anatoly Sagalevich, who designed the submersibles and participated in the expedition.
Scientists earlier Tuesday claimed to have descended 5,500 feet, which would have broken a record of 5,371 feet set in the 1990s.
But expedition leader Artur Chilingarov, a member of Russia's legislature, later said the record had not been broken. He also denied earlier reports that said one aim of the expedition was to break the world record for the deepest freshwater dive.
"We did not do this to break records," Chilingarov said, according to the Interfax news agency.
Russian media reports said Soviet scientists first descended into the waters of the lake in 1977, reaching a depth of 4,600 feet.
Sagalevich said the current mission will make a total of 160 dives in various areas of the lake over the course of two years. Organizers then will compile a list of recommendations for how best to preserve Lake Baikal.
In August 2007, the Mir-1 and Mir-2 descended below the North Pole, with Russians on board planting the country's flag in a titanium capsule on the Arctic Ocean floor to symbolically claim the seabed.
Chilingarov led that mission, too, receiving state honors on his return to Moscow.
