The indictment accuses David Hearn, 67, of "maliciously" breaking or destroying lining material on the bottom of the Reflecting Pool on June 19, causing more than $US1,000 ($A1,400) in damage.
The charge, brought in local Superior Court in Washington, DC, carries a maximum of 10 years in prison.
President Donald Trump and members of his administration have repeatedly blamed problems with the pool following a $US14.7 million renovation on vandals.
These have included blooms of algae and detached chunks of pool liner on the 610-metre-long) pool that runs from the Lincoln Memorial nearly to the Washington Monument on Washington's National Mall.
Trump has shown a personal interest in the project, and critics said the green-tinted water and peeling blue coating were emblematic of wider mismanagement by his administration.
The incident happened days after crews finished a Trump-ordered project to lay down new liner that Trump called "American flag blue" in time for celebrations honoring the 250th anniversary of US independence on July 4.
US Attorney for the District of Columbia Jeanine Pirro, a Trump ally, said during a news conference that Hearn "forcefully and violently" pulled on the pool liner on June 19 and shouted at a National Park Service employee who confronted him.
Park Police arrested him.
"This was a deliberate act to damage the Reflecting Pool at the National Mall that members of the National Park Service actually have worked hard to restore," Pirro told reporters on Thursday.
Lawyers for Hearn said he wais innocent and accused the Trump administration of using the case to provide "political cover" for mismanagement of the project.
"These charges are outrageous and should be alarming to every American," Hearn's lawyers, Norm Eisen and Mary Dohrmann, said in a statement.
"This indictment reflects the administration's effort to shift blame for their own failures."
Hearn previously acknowledged reaching into the pool while cycling in the area and told US media outlets that he tugged on a partially detached piece of liner, but did not remove anything.
Pirro said Hearn damaged about two square feet of the liner (0.2 square metres).
Trump said vandals made 250- to 350-foot-long cuts (76- to 107m) in the bottom of the pool, but has not provided evidence to back up those claims.
Asked about Trump's claims on Thursday, Pirro said someone caused extensive damage to the pool, but that investigators were still searching for those responsible.
The Department of the Interior has previously said at least six people were arrested on suspicion of vandalism following the renovation.
Hearn is the first to face criminal charges.
with AP
