Geotechnical drilling investigations began at the Sea Lift 7 barge.
State Premier Campbell Newman said the work is the first step in the project and will involve samples gathered by drilling at least 13 holes up to 60m deep into the river bed.
"The drill is located on a large barge that will move locations over the next few days between Lower River Terrace Park in Kangaroo Point and the City Botanic Gardens," Newman said.
Lawrence Springborg, main roads minister, added: "The tunnel will be carved from the earth by the largest, hard rock TBM ever used in Australia.
"A land-based drilling programme will commence at the end of January at various locations along the proposed alignment to confirm the depth and location of the tunnel and stations."
