Bach is leaving for the Brazilian city later in the day to attend celebrations marking the one year countdown to the Games on Aug. 5 and said pollution would be discussed with Rio 2016 officials.
Privately commissioned tests of the water quality where athletes will be competing revealed last week a high level of disease-causing viruses.
The waters along Rio's Atlantic coast, including Guanabara Bay where sailing events will be held, have been polluted for years and successive governments have spent hundreds of millions of dollars on attempted clean-ups to little effect.
"Of course this will be a topic like it is always a topic," Bach told reporters.
"The water pollution is a topic. What we have there and you have seen the test events going on, water tests are up to the Brazilian authorities."
Rio officials have started test events, including sailing, as they prepare competition venues for the first Olympics to be held on the South American continent.
"We have been informed by them (Brazilian officials) that they did the tests in accordance with the guidelines of WHO (World Health Organisation)," Bach added.
Biologists last year said rivers leading into the bay contained a superbacteria resistant to antibiotics that cure urinary, gastrointestinal and pulmonary infections.
When Rio bid to host the 2016 Olympic Games, the city trumpeted the clean up and said it would cut the amount of raw sewage flowing into the bay by 80 percent.
However, it has since admitted it is unlikely to meet that target, something Mayor Eduardo Paes called a "lost opportunity" for the city.
Earlier this year, the Rio de Janeiro state government said the amount of sewage treated before reaching the bay had risen from 17 to 49 percent.
(Editing by John O'Brien)
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