Walton said a juror asked his law clerk if the judge would advise what the charges are because some of jurors are "far afield" from what the actual charges are.
While expressing concern about jurors possibly discussing the case prematurely, Walton also said he had sympathy for the jury.
"When you create a boring environment which is being created in this case," Walton said, that will cause jurors to talk about the case "cause they're bored!"
Clemens, a seven-time winner of baseball's Cy Young Award, is accused of lying to Congress when he denied using steroids and human growth hormone.
Meanwhile, Walton dealt the government a defeat when he ruled it could not admit Clemens' baseball contract into evidence. Prosecutors wanted to use the contract to show the financial incentives Clemens had to take performance enhancing drugs to prolong his career, but the judge said that would invite jurors to speculate. He also said the contract could be prejudicial against Clemens, because some people think the salaries that pro athletes make is "obscene."
Walton said he saw both sides wasting time: He faulted prosecutors for showing a photo of Clemens and his wife in Sports Illustrated and defense lawyers for cross-examination of witnesses that went well beyond the scope of the government's questions.
"I'm putting you all on warning," Walton said, his voice rising. He told lawyers to stop throwing in everything but the kitchen sink and threatened to interrupt examination when he sees irrelevant questions being asked.
When jurors entered the room, Walton scolded them too, but more gently.
He told them it was brought to his attention by his clerk that there have been discussions about the nature of the charges, and reminded them they were not to have any discussions about the case. But he did say he appreciated that the trial was not moving as quickly as possible.
Just the day before, Walton urged both sides to pick up the pace, but it had no evident effect. Walton had complained Monday that there were a lot of unnecessary questions last week and warned, "if that continues, I will impose time limits."
The trial, which picked up a couple of miles per hour on its fastball last week with Andy Pettitte's testimony, has dropped back to a slow-pitch pace this week.
Prosecutors, who had said they might have star witness Brian McNamee testify Tuesday, now say there's no chance of that, and he might not even appear this week.
Monday's session was dominated by painstaking discussions about needles, syringes, gauze and cotton balls, how they had been stored and who had control of them. McNamee, Clemens' former strength coach, has said he saved those items from when he injected Clemens with steroids and human growth hormone.
The two government witnesses Monday were federal agents Jeff Novitzky of the Food and Drug Administration and John Longmire of the FBI. Novitzky began investigating connections between drugs and sports as an agent with the Internal Revenue Service.
Novitzky encouraged McNamee to cooperate with former Sen. George Mitchell, who was investigating performance-enhancing drugs in baseball, and Mitchell eventually identified Clemens as a user in his report to Major League Baseball.
"We thought it was a good idea for Brian McNamee to cooperate with Mitchell," Novitzky said, because government officials were concerned that kids were emulating pro players who were using steroids and HGH.
Clemens' lawyers focused on the condition of the evidence when it was handed over to authorities by McNamee, emphasizing a photo of the items bunched in a bag with a beer can rather than the photos of the items neatly arranged for classification once they were in the hands of the IRS and later the FBI.
Clemens' lawyer Michael Attanasio asked FBI agent Longmire about keeping evidence in a beer can.
"I would not," Longmire said.
"That's not what they trained us to do," the FBI agent responded.
The government is expected to show that Clemens' DNA was found among the items. Clemens' lawyers claim the evidence was tainted or contaminated.