The oldest part of the submerged forest is thought to date back to 3500 BC, although other sections, at Borth, near Aberystwyth, are believed to date back to 1500 BC.
It can be seen from near Aberystwyth to Aberdyfi and Tywyn up the coast in Gwynedd.
The lost civilisation of Cantre'r Gwaelod - or Lowland Hundred in English - was protected from the sea by a series of dykes and sluice gates.
One stormy night, legend has it that the appointed watchman Seithennin, a heavy drinker, was at a party and left the water gates open, the land flooded and disappeared under crashing waves.
Phil Hughes, chairman of the Friends of Cardigan Bay, said: "There is a lot of evidence to suggest that Cantre'r Gwaelod existed and I believe there was land out there.
"It will be the first time that it would have been seriously researched from an ecological point of view.
"The make-up of the area would have provided a natural barrier against raiders and shelter from the weather."
Mr Hughes said the most obvious sign that Cantre'r Gwaelod existed were the trees stumps that poked out of the water at low tide.
He added: "The primary aim of the project is to study the ecology of the sea bed in the area.
"We expect the project will last two to three years because the area measures some seven nautical miles."