The operation in a remote corner of the Algarve coast involved more than a dozen investigators using specialized climbing gear, including harnesses and ropes.
It is understood that the researchers found no evidence of Madeleine.
The wells are close to each other next to a narrow road that leads to Boca do Rio beach near the town of Budens, a half-hour drive from Praia da Luz, the seaside resort where Madeleine, three years, disappeared in 2007.
It is believed that the beach, one kilometer from the wells, was well known for Christian B, the German vagabond who is today the main suspect in the disappearance of Madeleine.
A photo of his VW camper van used in recent police calls was allegedly taken on the beach.
Plumber Jose Barata said he was driving along the road when he spotted police and firefighters and their vehicles parked next to the largest of the wells, which has the remains of an iron pumping engine at- above.
He said, “I slowed down my car when I saw a lot of police and firefighters near the wells and they told me to continue. I did not know what was going on.
“They were around a large well and the firefighters had ropes and other equipment. I thought it was some kind of rescue or maybe suicide.
“Later, someone I know told me that they had removed a lot of waste from the wells. “
Barata said he had followed the Madeleine case for 13 years and later realized, according to media reports, that the research was part of the investigation.
The vegetation around the wells had clearly been trampled on by investigators who had spent more than a day searching.
The land was sold three years ago by farmer Augusto Martins, who said the police hadn’t searched the area before.
The investigation into the alleged involvement of Christian B is being conducted by German prosecutor Hans Christian Wolters, who told Sky News last month that he wants to hear anyone with information about locations known to the suspect.
He says he has evidence that Madeleine is dead and insists that he is investigating a murder.
German and British police involved in the search for Madeleine have received nearly 2,000 reports since the call for public aid was launched five weeks ago.
A source said, “There are many avenues to follow, most of which will be of no use.
“But finding a well is a complicated matter and it suggests that the police were working on good, credible information. “