The congresswoman told the crowd she wanted to see a murder conviction against former police officer Chauvin for George Floyd's death last year.
When asked what should happen if Chauvin isn't convicted on murder charges, she replied, "We gotta stay on the street, we've got to get more active, we've got to get more confrontational, we've got to make sure that they know that we mean business."
Minneapolis is on edge as it anticipates the outcome of Chauvin's trial and reels from the death of 20-year-old Daunte Wright in Brooklyn Centre.
Judge Peter Cahill showed frustration with Waters' rhetoric shortly after the jury was dismissed Monday to begin deliberations. Chauvin's defence lawyer had motioned for a mistrial in light of Waters' comments.
Judge Cahill denied the motion but called it "disrespectful to the rule of law and to the judicial branch" for elected officials to comment on the outcome of the case.
"Their failure to do so, I think, is abhorrent, he said. "But I don't think it has prejudiced us with additional material that would prejudice this jury. They have been told not to watch the news. I trust they are following those instructions."
A spokesman for Waters didn't immediately respond to a message seeking comment.
Conservatives have seized on Waters' comments, saying she is inflaming tensions as Minneapolis looks to prevent looting and destruction that occurred after Floyd's death last year.
White House press secretary Jen Psaki was asked at Monday's daily White House briefing if Biden agrees with Waters' comment, but she attempted to tamp down the president's stance.
"He recognises the issue of police violence against people of colour, communities of colour is one of great anguish, and it's exhausting and quite emotional at times," she said, adding, "But as he also always says, protests must be peaceful. That's what he continues to call for."
The House Republican leader Kevin McCarthy said on Twitter that he was introducing a resolution to censure Waters "for these dangerous comments."
Senate Republican leader Mitch McConnell said in a speech that "it's harder to imagine anything more inappropriate than a member of Congress flying in from California to inform local leaders, not so subtly, that this defendant had better be found guilty."
House Speaker Nancy Pelosi said Waters' comments should be viewed in the context of the long struggle toward civil rights.
"Maxine talked about confrontation in the manner of the Civil Rights movement," Pelosi told reporters at the Capitol.
Asked if Waters should apologise, Pelosi said no.
"I myself think we should take our lead from the George Floyd family. They've handled this with great dignity, and no ambiguity or lack of misinterpretation by the other side," Pelosi said.