The DC Water authority said on Monday that it issued a permit to drain the pool, according to Reuters news agency.
The repair company has said it will fix the rectangular structure as part of its warranty.
BBC has contacted the DC Water authority and the National Park Service for comment.
The attraction was last fully drained in April this year for the Trump-inspired renovation, and refilled early this month.
The Reflecting Pool, built in the 1920s and stretching 2,030ft (619m) between the Lincoln Memorial and the Washington Monument, has long been beset by leaks, structural deterioration, faulty pipes, algae growth and bird droppings.
But despite the makeover, the pool has continued to be plagued by algae problems and developed issues with the deep blue paint Trump had added to its bottom.
In recent days, National Park Service staff have poured hydrogen peroxide into the water to try to get rid of the algae, while sections of paint are now appearing to peel off and float toward the surface, where visitors are scooping them out.
Trump on Monday echoed a threat from US Attorney for Washington DC Jeanine Pirro, who vowed to aggressively prosecute anyone found to have damaged the pool.
The president warned in a Truth Social post: “Please remember that there is a 10 year prison sentence for the destruction, or even the attempted destruction, of such things – Which will be fully enforced!”
Later in the day, he told reporters in the Oval Office that someone had cut a slit in the pool which he now thought was 350ft (107m) long and that “somebody said they might have put fertiliser there”, which had led algae to form.
Trump, who flew over the site in a helicopter while on his way back from Camp David, indicated a day earlier that the pool may need to be drained and refilled for a second time this month.
BBC News
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