The venue was last month described as a sewer by Britain's Sydney 2000 Olympic silver medallist Ian Barker due to its high levels of rubbish and stench, reports Xinhua.
Rio de Janeiro's state government Thursday said it would contract seven "ecoboats" to skim garbage off the water's surface.
"Are we going to improve the quality of the water? No. But we will decrease the risk that rubbish could affect the competition," Rio's environment secretary Carlos Coutinho said.
The government insists that Guanabara Bay's water quality does not pose a health risk to athletes.
But Coutinho admitted dirty water at the nearby Gloria marina and Botafogo bay, where competing vessels will be docked before racing, remains a concern.
Rio's government says it has treated about 40 percent of sewage in municipalities surrounding Guanabara bay.
During Rio's candidature in 2009, officials promised to treat at least 80 percent of wastewater by the time the Olympics begin Aug 5, 2016.