Members of Scotland Yard's underwater search team scoured Bedfont Lake, near London's Heathrow Airport.
Investigators acted after they received fresh information that a red Daewoo Nexia possibly used to transport her body was dumped there.
Police were spent most of the day searching a small fishing lake that forms part of Bedfont Lakes Country Park.
But a spokesman said “nothing of any relevance to the investigation has been found” and they do not plan to return to the scene.
The death of Amanda Dowler, known to her family and friends as Milly, remains one of Britain’s most notorious unsolved crimes.
The car was caught on CCTV in Walton-on-Thames minutes after the 13-year-old disappeared while walking home from school on March 21, 2002.
It was heavily laden and eventually reported stolen from a west London car park.
Six months later Milly’s skeletal remains were found 30 miles away by mushroom pickers in Yateley Heath, Hampshire.
The car has never been found despite exhaustive searches of scrap yards, lakes and scrubland over the past four years.
Prime suspect Levi Bellfield, who lived nearby, has admitted driving the car but claims he was carrying building materials.
Officers have been painstakingly building a case against Bellfield since he was arrested by the Metropolitan Police in November 2004 over other matters.
Bellfield, 41, was told last year that he would die in jail after he was found guilty of murdering students Marsha McDonnell, 19, and Amelie Delagrange, 22.
He was also convicted of the attempted murder of schoolgirl Kate Sheedy, 18. All of the women were attacked near bus stops in south west London.
The former nightclub bouncer and wheelclamper was arrested and interviewed over Milly’s death four years ago.
Officers believe they have compelling circumstantial evidence which links him to the crime.
Last month, Crown Prosecution Service solicitors were handed a dossier of evidence by Surrey Police and are considering whether to charge Bellfield with murder.
It emerged that detectives investigating Milly’s murder obtained new evidence, which cannot be disclosed for legal reasons, last December.
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