Searchers hope to have a clearer view of the bottom on Thursday.
Investigators trying to determine what happened to Holloway focused Wednesday on a pond near where the U.S. teen was last seen nearly two months ago.
Authorities used a large pump to drain the pond across from the Marriott Hotel while investigators awaited the results of DNA analysis from labs in the Netherlands and the United States.
The authorities declined to specify what they were looking for in the pond, but confirmed it was part of the investigation into Holloway's disappearance on May 30, the final night of a high school graduation trip to the Dutch Caribbean island. The job was expected to be finished later Wednesday.
A lawyer for Holloway's mother and stepfather said the search was prompted by a witness who came forward last week and reported seeing three young men, including a Dutch youth who has been detained in the case, near the pond on the night of the teenager's disappearance.
The witness told investigators that he saw Joran van der Sloot, 17, and two Surinamese brothers driving near the pond on May 30 between 2:30 and 3 a.m. a time they previously told investigators they were already home said the attorney, Vinda de Sousa.
"They consider the witness to be very credible," said the family's attorney, who said she receives regular updates on the case from investigators.
Holloway's stepfather, George Twitty, who was at a nearby hotel waiting for results of the search, said police asked the family not to watch as they worked behind a fence to clear the water.
"It's the first time the fire department, the police and other authorities have collaborated on such a huge search," the stepfather said Wednesday. "So they must know something. ... There's so much commotion, they must have a lead."
Holloway's mother, Beth Holloway Twitty, also said she was hopeful.
"I'm very encouraged about moving forward, and hopefully finding some answers that we've been waiting for, for a long time, and everyone has been," she said on ABC's "Good Morning America."