The cleaning of Guanabara Bay was a key part of Rio's bid pledge to host the Summer Games and has long been a goal of successive local governments.
Biologists in 2014 said rivers leading into the bay contained a superbacteria that is resistant to antibiotics and can cause urinary, gastrointestinal and pulmonary infections.
"We have tested the venue twice with more than 600 sailors so we know what needs to be done," Mario Andrada, communications director for Rio 2016, told Reuters during the United States Olympic Committee media summit on Tuesday.
"We need to fence the rivers so we don't have floating garbage into the bay. We need to keep the eco-boats oriented from above so they can spot the currents moving the floating garbage around so that the boats go there and take this garbage.
"And we are positioning the field of play, the regatta areas, on the outside of the bay, very close to the open ocean, so there is a strong current moving pollution and whatever away."
Additional measures have also been taken to reduced sewage and to purify the water, Andrada said.
"There is a new set of pipes around the Marina da Gloria so we are protecting that area from sewerage and from dirty water, he explained.
"And also we used bioremediation in two of the test events, the first one with great success, so we have everything we need to make sure the water is clean and more than that make sure there is no problem to the health of the athletes."
Bioremediation is a waste-management technique that uses microscopic organisms to break down contaminants.
Sailors for the German and British teams have already said they got sick after competing on the polluted waters and some racers have reported hitting floating waste, including a sofa and dead dog.
An inadequate sewage system and the untreated human waste that flows into the bay is one part of the problem, another is the illegal dumping of waste by companies.
However, Andrada drew confidence from the dramatic improvements shown during the test events for the Olympic sailing.
"The test events show that we are in the right place and during the Games we are going to test the water every single day," he said.
"In that way we will be able to shift the positioning of the regatta areas should we find a spot that is not as clean as the others. We are going to be in good shape."
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