Lionel Pousaz, spokesman for the Federal Polytechnic of Lausanne, said that final trials by submarines Mir 1 and Mir 2 were carried out at the lake on Tuesday and that the three-month-long exploration would begin Wednesday.
The two submarines have plumbed depths of more than 4,000 metres (13,000 feet) at the bottom of the Arctic ocean, and were also used to film the wreckage of the ill-fated Titanic and the Bismarck battleship.
The exploration of Lake Geneva, lying between France and Switzerland with a surface area of some 600 square kilometres (230 square miles), will focus on bacteria in the lake's sediments at a depth of more than 300 metres.
"The bacteria are indicators of pollution" and will help the scientists measure the presence of toxic elements, Pousaz said.
The mini-submarines, equipped with gauges capable of determining the density of molecules in the water, will also track micropollutants which may have escaped treatment plants.
These elements are expected to be found in the lake's plankton and fish.
In addition, scientists are planning to examine how water circulates in the lake by taking temperatures of different layers.
"A drop of water can take up to 12 years to cross the lake," Pousaz noted.