The nanobubblers had to go.

It was early June, and the Trump administration was planning an event at the Lincoln Memorial on June 12 to promote President Trump’s Ultimate Fighting Championship birthday celebration at the White House.

Dotted around the perimeter of the memorial’s Reflecting Pool were the nanobubblers, the temporary water-purification machines meant to keep the pool clear of algae. Encased in black fencing and powered by large generators, the machines were something of an eyesore.

Before the event, the National Park Service asked Greenwater Services, which won a $1.7 million no-bid contract to install the nanobubblers, to remove them, according to two people briefed on the decision. The people asked for anonymity because they feared retaliation from the administration. The Park Service did not provide a reason for the removal, but it coincided exactly with the promotional event, which drew crowds to the Reflecting Pool.

Photos from that evening showed the pool without the hoses or enormous machines working to keep the water clean. The water looked dark blue.

But by the time the purification systems were reinstalled 36 hours later, enormous algae blooms were starting to spread unchecked, turning the water green.

Once the algae started growing, it proved difficult to eliminate. Even with the nanobubblers back online, Park Service workers tried dumping jugs of hydrogen peroxide into the water to clear the algae more quickly. But the peroxide largely dissolved before it could reach the large clumps in the middle of the basin.

The result was a Reflecting Pool that stayed green and murky for about a week while nanobubblers cleared out the pea-colored residual chlorophyll — a highly visible symbol of one of Mr. Trump’s pet projects gone very wrong.

The decision to remove the water-treatment systems, which has not previously been reported, was one of several missteps that have plagued Mr. Trump’s $16.4 million renovation of the Reflecting Pool. There have been no-bid contracts, peeling strips of waterproof coating in Mr. Trump’s handpicked shade of “American flag blue,” and even a dead duck floating in the water (though it is not clear if the renovation had anything to do with the duck’s demise).

In recent days, the water has become clear again, reflecting the sky and the surrounding monuments. The temporary nanobubblers have been replaced with more discreet, permanent purification systems.

Still, the Park Service plans to drain the pool again soon to fix the peeling coating.

Taylor Rogers, a White House spokeswoman, did not answer specific questions, but said in an email that “thanks to President Trump, the Lincoln Memorial Reflecting Pool is fixed, crystal clear and currently reflecting beautifully ahead of America’s 250th birthday celebration.”

Mr. Trump has blamed vandals for the deteriorating conditions of the Reflecting Pool, saying they dumped fertilizer to feed the algae and slashed its blue coating with a “sharp knife or razors.” The administration has asserted in court that there were cuts made to the caulk and “surface material” of the pool.

Interviews with people involved in the project and a New York Times analysis — including a review of images taken by news photographers — suggest that actions taken by the Trump administration and the companies involved caused disruptions at every turn.

A Construction Spree

Mr. Trump has embarked on a construction spree in Washington unlike any undertaken by a modern president. He has rolled out jobs quickly, bypassing traditional contracting requirements and review panels. And costs have mounted as Mr. Trump’s vision for his most prized projects has doubled or tripled in size.

But it is the renovation of the Reflecting Pool that perhaps best serves as an emblem of how Mr. Trump operates. Instead of seeking competitive bids for the project, the administration awarded no-bid contracts, hoping to expedite the process. Mr. Trump never submitted the project to a review board so that experts could weigh in.

A crucial decision came in early April, when the administration awarded a no-bid contract to a Virginia-based company called Atlantic Industrial Coatings to spread the waterproofing blue coating on the pool’s concrete slabs. That coating, known as Rhino Pipeliner 5000, may be peeling off because it is not stretchy or flexible enough, said Anthony Flett, the chief executive of U.S. Coating Specialists, a Florida-based company that specializes in waterproofing substances.

“They used a hybrid polyurea, and they really should have picked a pure poly,” Mr. Flett said, adding, “There’s people in the pool industry whose whole life is polyurea, and they should have been called in.”

Tim Auerhahn, the chair of the Aquatic Council LLC, a consulting firm for the pool and hot-tub industry, said in an email that Rhino Pipeliner 5000 is usually used to line the inside of pipes.

“The manufacturer’s technical literature indicates it may be suitable for certain waterproofing and protective coating applications beyond pipe rehabilitation,” he said, “but it does not specifically identify large ornamental water features, swimming pools or granite-lined basins like the Reflecting Pool as primary use cases.”

Rhino Pipeliner 5000 is made by a California-based company called Rhino Linings. Pierre Gagnon, the company’s chief executive, said in an email that the peeling “is limited to isolated areas of the finish layer and does not affect the underlying waterproofing membrane.”

Representatives for Atlantic Industrial Coatings did not immediately respond to a request for comment.

As for the nanobubblers, problems with the generators caused issues with one or two of the four purification systems on June 15, according to government documents reviewed by The Times. But since then, the technology appears to have been working as intended, infusing the water with tiny bubbles of ozone gas to kill algae and bacteria.

Chas Antinone, the president of Greenwater Services, said in an interview on Friday that “we want people to understand that this is a cool technology. It’s clean and green. The only byproduct of this whole technology is oxygen.”

The ultimate owner of Greenwater Services is an investment trust led by John J. Cafaro, a donor to Mr. Trump and a neighbor to Mar-a-Lago, the president’s private club in Florida, The Times previously reported.

Mr. Antinone declined to comment on Mr. Cafaro’s role or the removal of the nanobubblers before the U.F.C. event. “I’m not the political guy,” he said. “I’m the science guy.”

Katie Martin, a spokeswoman for the Interior Department, the parent agency of the Park Service, said in an email that the nanobubbler technology “actively kills algae, pathogens (e.g., E. coli) and contaminants that have long plagued the Reflecting Pool since 1922.”

She added: “The current state of the crystal clear blue water is proof.”

David A. Fahrenthold contributed reporting.