What's killing the alligators of the Florida Everglades?

Alligators have thrived in the Florida Everglades for years, but scientists studying their population are now finding fewer and smaller gators.

"The best of them are skinny," said Frank Mazzotti, a wildlife ecologist with the University of Florida. "They weigh maybe 80 percent of what an alligator should weigh, but what is of greater concern to us is the proportion of alligators that are emaciated."

Mazzotti has been tagging and tracking alligators in the Florida Everglades for 15 years, and says the gator population there is now less than half of what you would expect in a healthy habitat.

"They're skinnier, they're fewer, they grow slower," Mazzotti said. "Most other places, if an alligator is 10 years old it's easily 6 feet long--not so in the Everglades. At 10 years [old], it's only 4 or 5 feet."

Mazzotti's team at the University of Florida is now investigating why the change is happening. He recently invited CBS News correspondent Bigad Shaban to join him on one of his research trips deep in the Everglades, about an hour north of Fort Lauderdale.

"Have you ever seen so many alligators in such poor condition?" Shaban asked.

"No," Mazzotti replied. "There's no flesh, it's just bones. Essentially it looks like a skeleton with skin hanging on it."

Shannon Estenoz is the federal government's point person on Everglades Restoration and says she is especially concerned about the declining health of alligators.

"When they are not doing well, something has gone wrong with the ecosystem." Estenoz said. "They are the canary in the coal mine."

Estenoz, who was appointed in 2010 by Secretary of the Interior Ken Salazar to serve as the agency's Director of Everglades Restoration Initiatives, believes the declining health of the alligators may be tied to a massive drainage project that first began in the Everglades decades ago. In order to develop what is now metropolitan South Florida, massive pumps were installed in the 1950s to drain much of the Everglades out into the ocean.

"Cities like Miami and Fort Lauderdale and West Palm Beach and other cities could not have grown in the way that they grew without this drainage project," Estenoz said. "It's the unintended consequences that it took us a few decades to figure out."

Scientists say the redirecting of water dramatically polluted and shrank the wildlife refuge. About a century ago, the Everglades stretched about 4 million acres, but today that's down to about 1.9 million acres.

"All of the flood protection and drainage infrastructure that was constructed within the last century to dry up land for that development has not only deprived the Everglades of actual habitat, but it's also redirected water from flowing through the Everglades out to the coast in unnatural patterns and with unnatural levels of pollution... mostly in the form of nutrients like fertilizer," Estenoz said.

A vast majority of the remaining Everglades footprint is now government-protected land and cannot be used for development, according to Estenoz.

While more than $20 billion dollars have been spent restoring the Everglades, there is no estimate on when the work will be done or whether it will be enough to snap the alligators back to health.

"No one set out in the beginning of the 20th century to destroy a world-class ecosystem," Estenoz said. "There was just a lack of appreciation and the understanding of the damage that was being done."