Health experts in Brazil have a word of advice for the Olympic marathon swimmers, sailors and windsurfers competing in Rio de Janeiro’s picture-postcard waters next month: Keep your mouth closed.

Despite the government’s promises seven years ago to stem the waste that fouls Rio’s expansive Guanabara Bay and the city’s fabled ocean beaches, officials acknowledge that their efforts to treat raw sewage and scoop up household garbage have fallen far short.

In fact, environmentalists and scientists say Rio’s waters are much more contaminated than previously thought.

Recent tests by government and independent scientists revealed a veritable petri dish of pathogens in many of the city’s waters, from rotaviruses that can cause diarrhea and vomiting to drug-resistant “superbacteria” that can be fatal to people with weakened immune systems.

Researchers at the Federal University of Rio also found serious contamination at the upscale beaches of Ipanema and Leblon, where many of the half-million Olympic spectators are expected to frolic between sporting events.

“Foreign athletes will literally be swimming in human crap, and they risk getting sick from all those microorganisms,” said Dr. Daniel Becker, a local pediatrician who works in poor neighborhoods. “It’s sad but also worrisome.”

Government officials and the International Olympic Committee acknowledge that, in many places, the city’s waters are filthy. But they say the areas where athletes will compete — like the waters off Copacabana Beach, where swimmers will race — meet World Health Organization safety standards.

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.

“It’s disgusting,” Mr. Monteiro said.

He has sailed past more than a few dead bodies, including the corpse of a man bobbing in the water last month, his legs bound in rope.

But Mr. Monteiro is most concerned with the shoreline factories that discharge chemical waste and the oil tankers that flush out their holds, giving the water’s surface a multicolored sheen.

As he pulled out from the harbor near his home on Governador Island, he pointed to a half-dozen pipes, exposed at low tide, belching out human waste from the island’s 300,000 residents.

“When you open up the fish, their innards are black with oil and muck,” he said. “But we clean them with soap and eat them anyway.”

For many residents, especially those who live in the slums, or favelas, the lack of sanitation causes misery. Hepatitis A is endemic among favela residents, health experts say, and children are frequently sickened by the pathogens that seep from sewage-laden culverts into jury-rigged drinking water pipes.

Irenaldo Honorio da Silva, 47, who leads the residents’ committee in Pica-Pau, a favela with 7,000 residents, said local officials had been promising to address the sanitation crisis for decades.

“They come, and then they go,” he said.

Heavy rains turn Pica-Pau’s streets into a putrid stew. One edge of the community is bounded by a fetid canal, its banks lined with homes, abandoned cars and food vendors.

The odor is overwhelming.

“This is nothing,” Mr. da Silva said. “In summer, it’s unbearable.”

Every few days, the State Environmental Institute tests bacteria levels in the city’s waters and posts them in a color-coded graph online. Many showcase beaches are consistently rated “unsuitable” for human activity.

That includes Flamengo, the bayside cove where the Olympic boating competitions will take place, and the iconic beaches that front some of Rio’s wealthiest neighborhoods.

Residents still throng the beaches on the weekend, but Prof. Renata Picão, a microbiologist at the Federal University of Rio, has refused to step foot in the water since she began sampling it three years ago.

Professor Picão has documented high levels of drug-resistant microbes at five of the city’s best-known beaches. The Oswaldo Cruz Foundation, a government-run lab, found superbacteria in the Rodrigo de Freitas lagoon, a body of water ringed by high-priced condominiums.

She said the pathogens, potentially fatal to those with compromised immunities, probably come from local hospitals that discharge untreated waste. Although superbacteria may not pose a threat to healthy people, the organisms can remain in the body for years and wreak havoc if a person becomes otherwise sick.

Professor Picão and other health experts say that unlike residents, who have been repeatedly exposed to sewage-borne pathogens, foreign visitors are more likely to fall ill after contact with contaminated waters.

And she is not optimistic about future cleanup efforts.

“If they couldn’t clean things up for the Olympics, a once-in-a-lifetime opportunity, I’m afraid it might never happen,” she said.