The Arade dam is 50 kilometres from Praia do Luz, where the British infant went missing 16 years ago.
The 45-year-old German national was designated an “arguido” by Portuguese prosecutors in 2022.
Brueckner visited the idyllic spot around the time Madeleine, now 20, disappeared.
Since Tuesday morning, police crews have erected tents all around the dam.
Officers from Portugal, Germany, and the United Kingdom are conducting morning briefings as divers assemble nearby. A boat is ready to take people into the reservoir, and sniffer dogs are patrolling the beach.
Braunschweig’s prosecutor’s office confirmed the search Tuesday morning but did not explain why.
Not for the first time has the reservoir been combed as part of the investigation.
In 2008, after receiving a tip from criminal sources that Madeleine’s body was in the water, the Portuguese attorney Marcos Aragao Correia hired scuba divers to search the waterway.
Three-year-old Madeleine from Rothley, Leicestershire, disappeared in Praia da Luz, Algarve, on 3 May 2007.
Her parents, Kate and Gerry, had gone to a resort restaurant for dinner with a group of friends, leaving Madeleine, her younger brother, and her younger sister to sleep in their apartment 100 yards away.
The parents devised a schedule to check on all of the children in the group throughout the evening. When it was Kate’s turn, however, she discovered that Madeleine had left.
Hans Christian Wolters, the German state prosecutor in Braunschweig, is treating Brueckner as the primary suspect in the McCann case, even though he has never been charged in connection with Madeleine’s disappearance and has denied involvement.
The state prosecutor stated that a growing body of evidence linked Brueckner to the case, including his mobile phone records indicating he was in the Praia de Luz region during Madeleine’s disappearance.
He lived near Praia da Luz when the McCanns vacationed there from 2000 to 2017.