Skirmishes between groups of protesters and law enforcement flared across the city on Friday and Saturday night as tensions played out over the death of George Floyd, an unarmed black man in Minneapolis who was pinned down by police.
Bowser stressed Sunday that protesters have the right to exercise the First Amendment but should not "destroy our city" in the process.
"We're sending a very clear message to people that they have a right to exercise their First Amendment rights, but not to destroy our city," Bowser said in an interview on NBC's "Meet the Press." "We saw a level of just destruction and mayhem among some that was maddening."
The DC Fire Department extinguished two vehicle fires in the area north of the White House Saturday night, as well as several small fires in the downtown area. Some protesters also put up graffiti on some buildings.
DC Chief of Police Peter Newsham said Sunday that the Metropolitan Police Department had arrested 17 people Saturday night and that 11 MPD officers were injured during the protests. None of the officers sustained life-threatening injuries, though one officer is undergoing surgery for multiple compound fractures to his leg after a protester threw a rock at him.
Newsham said that of the 17 people arrested, eight either live in DC or have some ties to the area.
He said police expect to make more arrests, as the department is asking private businesses to review their security footage, and will ask the DC community to help identify those who were damaging property or hurting people.
To this point, Trump has adopted an uneven message on the demonstrations. While in some appearances he has taken a measured approach in calling for calm, on Twitter he has used violent rhetoric and seemed to suggest on Saturday his supporters stage a counter-protest outside the White House.
Bowser on Sunday urged Trump to help "calm the nation" and to stop sending "divisive tweets that are meant to harken back to the segregationist past of our country."
That claim was later refuted by the US Secret Service who confirmed in a statement that the DC police department and US Park police were on the scene.
The DC mayor said while Trump "hides behind his fence afraid/alone," she stands with people "peacefully exercising their First Amendment Right after the murder" of Floyd and "hundreds of years of institutional racism."
Trump also tweeted that protesters "would have been greeted with the most vicious dogs, and most ominous weapons, I have ever seen," if they breached the fence outside the White House.
In a press conference Saturday, Bowser noted how Trump's reference to the "ominous dogs" was "no subtle reminder" of segregationists who would attack African Americans with dogs.
She added that the city is working on cleaning up after protests and is coordinating with law enforcement "to ensure calm in our city."
Newsham echoed that message Sunday, praising the behavior of police "incredibly responsible, heroic, in many instances," and said he doesn't expect Sunday night to be "a repeat of last night."
Still, a law enforcement source tells CNN that US Park Police, in a situational report Sunday afternoon, informed law enforcement stationed in Lafayette Park that demonstrators have brought boxes of rocks to an evening protest across from the White House.
Another person was observed with a bat, the report stated. The information was shared with other law enforcement agencies on hand for the protest, the source said.
Earlier Sunday, White House executive office staff received an email urging them to stay away from the White House complex, if possible, due to "ongoing demonstrations."
"Due to ongoing demonstrations, please avoid coming to the White House Complex today if at all possible," the email reads, in part. "The White House currently maintains an elevated security posture."
The email directs "essential" employees, who still need to work on the complex, to a specific entrance and to follow Secret Service instructions.
This story has been updated with additional developments.