Using diving teams and laser scanners operated from planes, 20 scientists from Germany, Austria and Switzerland are working to map the depths of Lake Constance, the 571-square-kilometre freshwater lake that the three countries share.
Since the first attempt to measure the lake in 1893, divers have pinpointed mysterious caverns in the underwater cliffs around the lake.
But the EU-funded project, costing €612,000, found some measuring up to 100 metres in width, with few clues as to what may lie within.
"Divers have always reported underwater holes there but this is the first time that we have located such large structures," the project's coordinator Martin Wessel told Die Welt newspaper.
Massive scarring observed on the lake bed also shows the course of the retreating glaciers after the last ice age, he said.
Other surprises include the wreck a 60-metre steamship, that was since identified as the Helvetia, scuttled in 1933.
Measuring 63 kilometres in length and up to 14 kilometres wide, Lake Constance is Central Europe's third largest body of inland water after Lake Balaton and Lake Geneva. At its deepest point it is 252 metres.