Raw sewage, industrial runoff, trash, algal blooms. Each has plagued Guanabara Bay, the site of the sailing events at this summer's Olympics in Rio. Although local officials have taken pains to try to sanitize the water ahead of the Games, those efforts have fallen short of Olympic organizers’ and athletes’ expectations. Unsurprisingly, some Olympians are on edge. Sailors preparing for windsurfing or one-person dinghy events, for example, must overcome an extra hurdle: They must attempt to steer clear of refuse and avoid diarrheal disease as they race on the area’s famous waters.

The coastal area around Guanabara Bay is home to about 16 million people, and tons of their untreated raw sewage is discharged into the water each day. Solid waste is visible in some areas, bobbing along the water’s edge.

Still, “Rio 2016 and all relevant local authorities are confident that the venue will be ready to host the Olympic sailing competition in August 2016,” the International Olympics Committee wrote in a statement to Scientific American. The city has reduced industrial pollution and floating waste, increased water treatments and completed an $11-million effort to erect barriers to stop debris from entering the bay ahead of the sailing events, they wrote.

Alberto Chebabo, president of the Society of Infectious Diseases of the State of Rio De Janeiro, spoke with Scientific American’s Dina Fine Maron about the state of the bay and the health threats to athletes who will be exposed to it.

[An edited transcript of the interview follows.]

What can you tell me about the area of Guanabara Bay where Olympians will be sailing or windsurfing in August?

At this time of the year—July and August—we have a very dry season in Rio. We have waters from the ocean entering the bay and washing it so it’s cleaner than it usually is. So if it doesn’t rain, the bay will probably be okay where the competition will be held. But it’s still not clean. This bay is never okay for swimming, I would not recommend that, but the athletes will be in boats so they’ll have less contact with the water.

Scientists have documented that large amounts of untreated sewage and industrial waste from refineries and pharmaceutical plants are dumped into that body of water and that solid waste is visible at some places on the bay’s margins. What do athletes need to be concerned about?

The major problem is ingesting the water. The athletes will not be swimming in this water but they will still get wet. Contact with the skin —casual contact—will not be a problem. If the athlete has cuts, however, infection could be a concern as there are many bacteria associated with such infections, like Pseudomonas, Vibrio and others.

We have bacteria and viruses that can cause diarrheal diseases, that is the most common issue. We also have hepatitis A so people should get vaccinated for that before coming here to compete. Even in the bay’s best conditions the water is contaminated with bacteria and viruses from sewage.

How much water would a person need to ingest to get sick?

It depends. If the person had previous contact with the water, they will have some antibodies to those bacteria and viruses. The ones who are having their first contact with the water could become sick more easily—with less water contact—than someone who has been in this water before. Of course it depends person to person but I think 100 milliliters or less would be enough to make them sick. But most of the athletes that are here for the Olympics have been here before—for other competitions—or they may have had some similar exposures in the water in their home countries. These issues are not unique to Rio.

What specific pathogens are in the water?

We have some pathogenic and nonpathogenic bacteria in these waters. We have some pathogenic bacteria like Vibrio, which causes diarrhea. We have Shigella, which can cause disease in humans, mainly diarrhea. There are also oil and solvents from nearby industry but the amount of water these athletes would ingest would be too low to be concerned about those. The major problem is the bacteria from the sewage.

What is the latest research about antibiotic-resistant bacteria found in the water?

Klebsiella pneumoniae carbapenemase (KPC)is the only multidrug-resistant bacteria found in studies published about Guanabara Bay. Some researchers detected KPC in some areas of the bay and at beaches outside the bay. They also found KPC-producing bacteria in a river that flows into the bay. We don’t know exactly what that means for human health. Of course it’s a resistant bacteria, but this kind of bacteria hasn’t caused disease in healthy people, at least that we know of until now.

An Associated Press investigation found bacteria and viruses including adenovirus, rotavirus and enterovirus in the bay. Are there any more recent or peer-reviewed investigations?

We don’t have too many studies on the viruses in the water. We know there are viruses and bacteria because there is sewage and we know there is sewage because a local agency takes fecal chloroform counts. Those counts are the easiest way to monitor the water and see if it is contaminated or not.

I was startled to read that 65 percent of hospital visits among a low-income segment of the population living close to the bay are due to water-borne diseases. That's 2005 data, however. What’s the recent data?

We don’t have too much data about this. There are a lot of cities around Guanabara Bay and the poorest areas are in the back of the bay, and that’s where a lot of these issues are. There are areas where the sewage flows directly to the river and from there to Guanabara Bay, and that’s where we have a lot of problems with waterborne diseases and poor sanitation.

What can athletes do to protect themselves? Should they preemptively take medications or take some other precautionary measures?

Hepatitis A vaccination is important. But most, if not all, of the athletes have this vaccination before coming to compete here. They should also clean themselves and their clothes after competition.

Otherwise they should just watch what they eat and drink and wash their hands. It would be worse to take an antibiotic like ciprofloxacin before competition because cipro can change their gut flora. Our gut flora protects against other bacteria that try to invade our system.