(CNN) The most terrifying thing lurking under the waters of the Atlantic Ocean may not come with razor sharp teeth.

Scientists say Florida's coral reef system, the third-largest in the world, is in rapid decay, with a variety of threats edging the delicate ecosystem closer to collapse sooner than anyone believed possible.

"We didn't think this would happen for another 50 or 60 years," said Chris Langdon , a marine biologist at the University of Miami, who published a new report on the health of the reef in May. "This study showed a whole new thing we didn't even know was threatening them."

Langdon and his team discovered that as ocean water becomes more acidic, due to carbon dioxide levels in the atmosphere, the structures that support the coral are beginning to disintegrate.

A diver with Project Baseline collects samples from Hollywood Beach sewage outflow, which pumps millions of gallons of effluent into the ocean every day.

A diver with Project Baseline collects samples from Hollywood Beach sewage outflow, which pumps millions of gallons of effluent into the ocean every day.

A project baseline team dives more than 90 feet to inspect sea life around the Hollywood Beach sewage outflow.

A project baseline team dives more than 90 feet to inspect sea life around the Hollywood Beach sewage outflow.

The Hollywood Beach sewage outflow is roughly 5 feet in diameter and at one point pumped more than 47 million gallons of effluent a day. Officials with the city of Hollywood say they have reduced that rate in recent years, down to 12 million gallons a day. The outflow is slated to shut down in 2025.

The Hollywood Beach sewage outflow is roughly 5 feet in diameter and at one point pumped more than 47 million gallons of effluent a day. Officials with the city of Hollywood say they have reduced that rate in recent years, down to 12 million gallons a day. The outflow is slated to shut down in 2025.

Project Baseline divers analyzing ocean life near the Hollywood Beach sewage outflow. Much of the ocean floor in this area is covered by invasive algae, which some experts believe has spread expansively in part because of nutrient loading.

Project Baseline divers analyzing ocean life near the Hollywood Beach sewage outflow. Much of the ocean floor in this area is covered by invasive algae, which some experts believe has spread expansively in part because of nutrient loading.

Project Baseline and a CNN team review safety procedures before diving more than 90 feet to reach the outflow. It takes roughly 25 minutes to reach that depth.

Project Baseline and a CNN team review safety procedures before diving more than 90 feet to reach the outflow. It takes roughly 25 minutes to reach that depth.

The Baseline Explorer, one of Project Baseline's vessels, is harbored just outside Port Everglades in Fort Lauderdale. While coral bleaching due to warmer water brought on by climate change and the spread of viruses that can damage coral have played a role in the reefs decline, Robert Carmichael, a member of the the group, says some factors can be quickly and directly addressed, including nutrient loading from outflow pipes and dredging of the ports.

The Nemo submarine reaches the surface after an hour-long dive. Crews move quickly to reattach the submarine to a crane onboard the Baseline Explorer. When out in the sun, temperatures on the Nemo near 100 degrees.

The Nemo submarine reaches the surface after an hour-long dive. Crews move quickly to reattach the submarine to a crane onboard the Baseline Explorer. When out in the sun, temperatures on the Nemo near 100 degrees.

Diver Robert Carmichael preparing to dive to the Hollywood Beach sewage outflow, just one mile from shore, with CNN correspondent Boris Sanchez.

Diver Robert Carmichael preparing to dive to the Hollywood Beach sewage outflow, just one mile from shore, with CNN correspondent Boris Sanchez.

Robert Carmichael, a diver with Project Baseline, reviews procedures with CNN correspondent Boris Sanchez while preparing to dive to the Hollywood Beach sewage outflow in the Nemo -- a Project Baseline submarine.

Robert Carmichael, a diver with Project Baseline, reviews procedures with CNN correspondent Boris Sanchez while preparing to dive to the Hollywood Beach sewage outflow in the Nemo -- a Project Baseline submarine.

The acidification process occurs because during the carbon cycle -- nature's way of processing carbon -- the ocean absorbs much of it. As more fossil fuels are burned, sea water mixes with carbon dioxide and becomes carbonic acid. Because there's excess carbon dioxide, the ocean cannot process it as well as it used to -- and it ends up becoming more acidic.

"When you add acid to a piece of limestone, you'll see it fizz up. That's what we're talking about here," said Langdon. "We can definitely see less each year, less coral than the year before."

Though research on acidification's effect on the reefs is still relatively new, Langdon says it is only the latest in a series of factors harshly impacting the delicate underwater habitat.

Smothered by algae?

"It's all the pressures combined that are destroying this," said Robert Carmichael, who works for Project Baseline , a nonprofit that documents changes in underwater environments around the world.

Carmichael says that since he started diving at the Florida reef more than 30 years ago, 93% of the hard coral in the area has vanished.

"It's not just pretty to look at; this is vital to our own lives," he said. "It makes me sick to my stomach."

The life of the reef is critical, he said. The fishing and tourism industries rely on the reef and it acts as a barrier to limit harsh wave activity on the coast, an important factor during hurricane season.

"The more you study the ocean, the more you realize we are perfectly connected to the oceans as humans. Our life does depend on it," he said.

While coral bleaching due to warmer water brought on by climate change and the spread of viruses that can damage coral have played a role in the reefs decline, Carmichael says some factors can be quickly and directly addressed, including nutrient loading from outflow pipes and dredging of the ports.

Along with dozens of scientists and volunteers at Project Baseline, Carmichael has done extensive work to examine the impact that six sewer outflows along the Florida coast have had on the coral reef.

"If the vast majority of tourists knew that they were swimming in this, I think they might reconsider where they go for their vacations," Carmichael said. "Most people simply don't believe this occurs."

According to Carmichael, the outflows dump hundreds of millions of gallons of waste into the ocean every day, including substantial amounts of phosphorus, nitrogen and other substances that have made the reefs "so grossly out of balance and under attack that they don't stand a reasonable chance of recovering."

Carmichael says that "nutrient loading," or the dumping of chemicals into the ocean water, has strengthened the coral reefs mortal enemy: Algae.

"It's actually become the dominant species on the reef," said Carmichael, who says the algae covers the ocean floor and smothers the reef by blocking sunlight.

"It's like a constant beating and eventually, the reef lost," he said.

Officials at the city of Hollywood, where one of the outflows is based, says the connection between sewage outflows and coral reef decline is murkier than Carmichael's analysis, though.

Raelin Storey, a spokeswoman for the city, says she does not believe the ocean outfall is "the primary source of all problems with the coral reefs."

Citing research from the National Oceanic and Atmospheric Administration , Storey says that no conclusive link has tied the disappearance of the reef with the Hollywood outflow, though she adds that she is generally concerned with the water quality in the area and says the outflow should be shut down.

The coastal outflows in Florida were scheduled to be shut in 2017, following a push from Florida's Department of Environmental Protection, but the plan was delayed, allowing them to remain running until 2025.

"We are making every effort to reduce those flows," Storey said, also saying that the city follows all state regulations and has spent millions of dollars to improve water quality.

Controversial projects

Another controversial issue that environmentalists say has weakened Florida's reefs: Port dredging.

"We are seeing these reefs disappear before our eyes," said Rachel Silverstein, executive director of Miami Waterkeeper , a nonprofit dedicated to preserving marine ecosystems and water quality across South Florida.

According to Silverstein, a multiyear project to deepen the port of Miami "buried alive over 200 football fields (worth) of our coral reefs off Miami Beach," including species of coral that are on the endangered species list.

"We will never get back the reef that was lost," she said. "I think we need to take extreme measures at this point to protect every last coral that we can."

After the project was completed in 2015, Miami Waterkeeper sued the U.S. Army Corps of Engineers, claiming it violated the Endangered Species Act.

"I think they vastly underestimated the amount of damage they were going to cause," said Silverstein. "When they noticed how much damage was being done, they failed to take any steps to mitigate what they were doing."

Miami Waterkeeper is now also concerned about a similar dredging project set to kick off in 2017: the dredging of Port Everglades , fewer than 40 miles north of Miami.

Silverstein says that despite the lawsuit and vocally raising concerns, the Army Corps of Engineers "have not done anything that we have been recommending."

In response to the lawsuit, a spokesperson for the Corps sent CNN a statement that reads, in part: "There's a tremendous amount of erroneous information in the media that's almost entirely facilitated by a few critics and supported by a large environmental media group that are propagating the misinformation. This disregard for the facts is totally misleading the public."

According the statement, the effects of dredging have been greatly exaggerated and do not threaten the overall viability of the reefs, only affecting a portion that spans less than half a square mile.

The statement also indicates that the Army Corps of Engineers "have incorporated lessons learned from Miami Harbor and other projects" that they will use when dredging Port Everglades.

Far-reaching effects

Despite the mounting controversies about what is weakening Florida's coral reefs, scientists warn the consequences of letting the trend continue could be staggering.

"People who don't live as close don't care as much, but they should get the message they are going to be affected as well," said Langdon. "It's going to affect our economy, it's going to affect our jobs."

According to NOAA's website , the corals bring in about $8.5 billion to Florida's economy, helping to keep about 70,000 people employed.

"The straw is going to break the camel's back," said Langdon. "If you're getting eaten away by cancer, you want to attack it right away before the tumors get too big... We've got to wake up and do something."