From doping scandals to security concerns, the 2016 Olympic Games in Brazil has been embroiled by one crisis after another—and that's just the tip of the iceberg.

As athletes and hundreds of thousands of tourists around the world descend into Rio de Janeiro, here are seven health and environmental controversies that have already made headlines before the Aug. 5 Opening Ceremony.

The polluted Guanabara bay in Rio where rowing and sailing will be held.Flickr

1. Polluted Waterways

Rio's epic water pollution has been going on for two decades due to a lack of modern sanitation programs. Despite Olympic organizers's promise to clean the city's waterways at their 2009 bid, trash, raw sewage and even body parts have been a presence at water sport venues.

At Guanabara Bay—where rowing and sailing will be held—tons of noxious raw sewage gets pumped into the bay each day. Oceanographer David Zee told CBS News that the Brazilian government planned to install eight treatment plants on Rio's polluted rivers but only built one. Officials promised to treat 80 percent of the sewage flowing into the bay but have gotten to only half. USA Today Sports reported that organizers will use a short-term and (purely cosmetic) water treatment method so the waters will glisten blue for television broadcasts.

In fact, Rio's Olympics will bring none of the environmental improvements that were originally pitched. An official from Brazil's Federal Audit Court, which audits the federal government's spending, told Reuters: "As for now, we have nothing relevant to report about what was done in the environmental area."

2. Super Bacteria

In related news, last year, the Associated Press published its results from an eight-month study of Rio's water venues, concluding that none were safe for swimming or boating, with more than 1 billion viruses from human sewage in a single liter of water from the Rodrigo de Freitas Lake. Water samples were 1.7 million times the level of what would be considered hazardous on a Southern California beach.

That leads us to this conundrum. As EcoWatch mentioned last month, antibiotic-resistant super bacteria has been found in waters that will host the swimming portion of the triathlon and in the lagoon where rowing and canoe athletes will be competing. Two studies have connected five beaches—Copacabana, Ipanema, Leblon, Botafogo and Flamengo—and the Rodrigo de Freitas to the superbug bacteria. Scientists say the super bacteria can cause hard-to-treat urinary, gastrointestinal, pulmonary and bloodstream infections, which contribute to death in up to half of infected patients. Meningitis has also been linked to exposure to the superbug.

3. Zika

A number of high-profile athletes, especially golfers, have dropped out of the Summer Games due to Zika fears. The mosquito-borne virus, which has spread throughout the South American country, has been declared an international public health emergency by the World Health Organization. Some scientists have suggested that global warming is exacerbating the problem, which is linked to microcephaly in babies. Infectious diseases, such Zika and dengue, could spread as aedes aegypti mosquitoes expand their habitats in a warmer, wetter world, one study found. Experts, however, have said that there is little risk of Zika spread. The southern hemisphere is also currently in the middle of winter, making the threat of bites even lower. Still, the epidemic has only further impaired Brazil's struggling public health system, and will continue be a problem when the games conclude.

4. Golf Course Trampling on Nature

Golf's return to the Olympics should have been celebrated. However, not only are some of the sport's biggest stars skipping Rio due to Zika, instead of using the city's two existing golf courses, organizers decided to build a completely new one from scratch. Biologist and environmental activist Marcello Mello told the Guardian that the new course encroaches on the Marapendi reserve, home to rare butterflies, pines and other species not found anywhere else in the world, calling the construction an "environmental crime."

"They are destroying the Atlantic Forest, which is part of our national heritage," he added. Mello also alleges that the city is using the Olympics to help foster business for development companies. "Without a doubt, the Olympics are a giant real estate scam," he said. This is not to mention that thousands of people living in Rio's favelas have been notoriously pushed out of their homes for Olympic construction.

5. Jaguar Killing

Last month, a jaguar—the Brazilian Olympic team's mascot—was shot and killed at the Olympic torch passing ceremony. As EcoWatch reported, the female jaguar was shot after the female jaguar escaped from her handlers, sparking outcry from animal activists.

"Wild animals held captive and forced to do things that are frightening, sometimes painful and always unnatural are ticking time bombs—captivity puts animal and human lives at risk," the People for the Ethical Treatment of Animals wrote in a blog post.

Jaguars are a near-threatened species with an estimated 15,000 left in the wild, according to Defenders of Wildlife.

6. Public Transportation Mishaps

When Rio organizers made their bid for the summer games seven years ago, they suggested a number of improvements to ease the city's terrible traffic, which causes severe congestion, noise and air pollution from vehicle exhausts. However, the organizers probably did not anticipate that a crippling recession would affect their plans. The city's government declared a state of financial disaster last month, impacting Olympics-related infrastructure projects.

Rio's new 10-mile rail line, which cost $1.2 billion more than its initial estimate, may not be completed in time before the opening ceremony. A bike lane collapsed in April, killing two people. And according to the Associated Press, the new light rail system suffered a major power outage on the second day of service and the month-old highway near Barra da Tijuca is already damaged with potholes and large cracks.

7. The Danger of Environmental Activism

Protesting any of the environmental or health issues above might be a danger in itself. Brazil happens to be the nation of the highest death toll of environmental activists. Global Witness revealed 50 confirmed murders of environmental activists last year.

"I know there is a risk to this work. It is dangerous to campaign for the environment in Brazil," Mello told the Guardian about his Occupy Golf Campaign. "But I love nature and somebody has to do this job. If I die for this cause, it will be worth it."