Even some venues with higher levels of human waste, like Guanabara Bay, present only minimal risk because athletes sailing or windsurfing in them will have limited contact with potential contamination, they add.  Still, Olympic officials concede that their efforts have not addressed a fundamental problem: Much of the sewage and trash produced by the region’s 12 million inhabitants continues to flow untreated into Rio’s waters.  “Our biggest plague, our biggest environmental problem, is basic sanitation,” said Andrea Correa, the top environmental official in the state of Rio de Janeiro. “The Olympics has woken people up to the problem.”  Foreign athletes preparing for the Games have long expressed concern that waterborne illnesses could thwart their Olympic dreams. An investigation by The Associated Press last year recorded disease-causing viruses in some tests that were 1.7 million times the level of what would be considered hazardous on a Southern California beach.  “We just have to keep our mouths closed when the water sprays up,” said Afrodite Zegers, 24, a member of the Dutch sailing team, which has been practicing in Guanabara Bay.  Some athletes here for the Games and other competitions have been felled by gastrointestinal illness, including members of the Spanish and Austrian sailing teams. During a surfing competition here last year, about a quarter of the participants were sidelined by nausea and diarrhea, organizers said.  Officials have been grappling with a welter of challenges as they scramble for the opening ceremony on Aug. 5. The Zika virus epidemic has dampened foreign ticket sales, crime is soaring, and the federal government has been paralyzed by the impeachment proceedings against Brazil’s president, Dilma Rousseff.  Last month, the acting governor of Rio de Janeiro, Francisco Dornelles, declared a state of emergency, claiming that a lack of money threatened “a total collapse in public security, health, education, transport and environmental management.”  Still, Olympic organizers say the sports venues are nearly complete, and the federal government has provided emergency funds to the state. Many athletes expect the Games to proceed without serious complications.  The city’s contaminated waterways, however, are another matter.  “It’s disgusting,” said Nigel Cochrane, a coach for the Spanish women’s sailing team. “We’re very concerned.”  For many, the sewage crisis is emblematic of the corruption and mismanagement that have long hobbled Brazil, Latin America’s largest country.  Rio officials claim to have spent billions of dollars on sewage treatment systems since the 1990s, but few are functioning.  In its 2009 bid for these Games, Brazil pledged to spend $4 billion to clean up 80 percent of the sewage that flows untreated into the bay. In the end, the state government spent just $170 million, citing a budget crisis, officials said.  Most of the money in the state’s sanitation budget has been spent on trash-collecting boats and portable berms to stop the sludge and debris that flow into the bay.  Critics say they are cosmetic measures.  “They can try to block big items like sofas and dead bodies, but these rivers are pure sludge, so the bacteria and viruses are going to just pass through,” said Stelberto Soares, a municipal engineer who has spent three decades addressing the city’s sanitation crisis.  Mr. Soares said he laughed when he heard officials promise to tackle the sewage problem before the Games.  An earlier, multibillion-dollar effort financed by international donors yielded a network of 35 sewage treatment facilities, 500 miles of conduits and 85 pumps, he said. When he last checked, only three of the pumps and two of those treatment plants were still working; the rest had been abandoned and mostly vandalized, he said.  Asked what had happened, he threw up his hands. “In Brazil, they say sanitation doesn’t get votes,” he said.  Romario Monteiro, 45, a second-generation fisherman who has spent a lifetime plying Guanabara Bay, recalls when the waters were crystalline and the fish were plentiful.  Now his net often yields more trash than fish, including television sets, dead dogs and the occasional dolphin killed by ingesting plastic bags.
Sewage and trash continue to flow untreated into Rio de Janeiro’s waters, and recent tests found pathogens including rotaviruses and drug-resistant “superbacteria.”