President Donald Trump has threatened prison time for anyone caught damaging the pool.
The DC Water authority issued a permit to drain the 609-metre rectangular pool, it said on Monday, while the repair company said it would fix the pool as part of its warranty.
The National Park Service did not immediately respond to a request for comment.
Peeling paint and algae growth have been visible in the pool since soon after Trump declared the renovation project complete on June 6.
Critics have raised concerns about the no-bid contract to recoat the pool before the nation's 250th anniversary celebrations next month, as well as for the ducks that use its water.
Workers from the National Park Service earlier this week poured hydrogen peroxide into the pool to combat the algae.
Trump, without evidence, has blamed vandals for the state of the landmark.
On Monday, he echoed a weekend threat by US Attorney Jeanine Pirro to prosecute people accused of attempting to destroy the pool.
"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!" Trump earlier wrote in a social media post.
Destruction of federal property can carry a maximum prison sentence of 10 years.
Trump told reporters on Monday that the pool "looks very good".
He accused someone of putting fertiliser in the water or taking action to create the algae, without providing evidence, adding that the algae was now dead and would be vacuumed out of the pool.
Trump also said there was a 90 metre "slit" through the pool, which he said was likely caused by a box cutter or knife of some kind.
"It's not a lot of damage, but ... we'll probably have to let the water out and re-fix it. They went in there with a knife," he said, without providing evidence.
At least five people have been arrested, including a former Olympian who publicly denied the charges, while five others were issued citations, according to media reports citing an administration official.
The company responsible for the renovation work, Virginia-based Atlantic Industrial Coatings, said on Sunday the areas that required repairs made up "a very small part of the massive 7-acre (2.83-hectare) project, and do not indicate a failure of the liner".
