Small Bonefish in the Florida Keys are Coming From the Gulf Stream

April 21, 2020 By Bruce Chard

This article was originally titled The Bones are Back: Small bonefish in the Florida Keys are coming from the Gulf Stream. It appeared in the April-May 2020 issue.

In 1992 I was 18 years old and working as a Bell Captain at Leona Helmsley’s South Lido Key Florida Beach resort, called the Harley SandCastle. That’s when I when I fell in love with saltwater fly fishing. I Learned to tie flies Tuesday nights at the Orvis shop on Siesta Key. I met a lifelong fly-fishing buddy who taught me how to cast and tie knots. He introduced me to bonefishing in the Florida Keys. On our first visit to the Keys, we camped at Long Key State Park and found ourselves fishing to huge tailing bonefish right in front of our campsite. It was then I knew I would move to the Keys to pursue my goal to become a fly-fishing guide.

Six weeks later I was living on Big Pine Key, learning the waters from Marathon to Key West. I immediately started bonefishing all over the Keys, consistently experiencing acres and acres of tailing bonefish on popular flats from Key Largo to the Marquesas. At that time I believed that the Keys had some of the best big bonefishing in the world.

The number of boats and fisherman on the water was light. The catch-and-release bonefishing tournaments in Islamorada commonly recorded bonefish over 12, 13, and 14 pounds. It seemed that a potential world record bonefish could be caught on any given day. On the rare occasion that we landed a fish that was under 25 inches, it was considered small. Then came 1998.

Boom and Bust

In 1998 the housing market in the Keys was booming, dramatically increasing the population along this tiny strand of limestone and oolite. This surge in construction resulted in more boat traffic and more fishermen on the water.

In September 1998, Hurricane George made landfall in the Lower Keys. After the storm, a good friend of mine needed some help cleaning his yard. He noticed that his in-ground swimming pool that was about 20 feet from his seawall must have a leak somewhere, as he was losing water. In order to find the leak, he dumped red dye into the pool water, and it didn’t take long for the nearby canal to turn red as well. The pool water was leaking out of the crack and into the porous Lower Keys fossilized caprock and right into the salt water of the nearby canal.

It was then clear to me how much impact Keys residents have on this sensitive ecosystem. It explained why at my house on Big Pine Key, my plumbing would sometimes back up when heavy rain or high full-moon tides would not allow my leach field in my septic tank to drain properly. And it wasn’t just my house. Everyone’s house had leaching septic fields that backed up during high tides and drained on low tides. There was no doubt that systems of this type were contaminating our waters daily.

Immediately after Hurricane George, the bonefishing started to change. I don’t know if it was all the new houses that had been built in the previous few years, or the fact that the hurricane had cleaned out everyone’s septic systems, but after 1998 things started to go downhill. There were fewer bonefish, and some particular bonefish flats just went dormant with no bonefish at all.

The Florida Keys suffered decreasing bonefish numbers every year from 1998 until the “big freeze” of 2010, when they hit rock bottom. Now things are turning around. Jeff Edvalds photo

As the years passed, there were more houses—all with their own septic systems and leach fields—and more vacationers and more angling pressure, but every year, fewer and fewer bonefish. In 2005, housing in the Keys was at its peak. It didn’t seem there was anywhere left to build, and in October, Hurricane Wilma rolled through the Keys with a very strong storm surge.

Then in January 2010 came a dagger to the heart. A weather anomaly happened, causing three back-to-back-to-back cold fronts to roll through the Florida Keys. Usually when cold fronts move through the Keys there is a warming period before the next front rolls through. In this circumstance, three cold fronts moved through so close together that water temperatures in Florida Bay dropped into the upper 30s. The cold fronts caused fish kills that crushed shallow-water gamefish across the state of Florida.

Bonefishing had been in decline for a decade, but after 2010 it was decimated. Many guides theorized that even the food bonefish eat on the flats was killed by low water temperatures, forcing the remnant bonefish population to Key West areas, where the impacts were less severe.

Interestingly, there was an influx of redfish that moved onto Keys flats in the years after the big freeze. The Keys has always had some redfish, but never like this. It seemed that water quality in the Everglades and in South Florida had gotten so poor, redfish were forced south to the Keys to survive.

Back in 1999, all Florida Keys municipal sewage went to shallow injection wells, septic tanks, leach fields, and in some cases cesspits. In that year, the state of Florida ordered Monroe County to build a contained wastewater sewer system. It took a decade to get funding, buy land, and begin construction, but by 2011 a multiyear project to improve Keys water quality began. It was a $1 billion project that included $170 million in state and federal aid. By 2017 the last major wastewater facility was completed in the Lower Keys, and more than 80 percent of the county’s 77,000 residents were connected to it.

Although Monroe Country has solved its municipal sewage problems, water quality in the Florida Keys continues to be a problem, with agricultural and residential wastewater coming from the mainland. Jeff Edvalds photo

Interestingly, as sections of the sewer system were completed, and more and more residents hooked up to it, we began to see more and more bonefish on the flats, and most of them were much smaller than we had seen in the glory days.

By 2018 I noticed the largest increase of bonefish numbers I have seen in the Keys in over a decade, and there were some larger fish mixed in as well. These bonefish seemed to be less migratory in their habits, and would often just hang around certain flats, tailing and feeding. They seemed happy and comfortable.

It seemed like an incredible coincidence to me that the bonefish numbers seemed to decline when our local wastewater was going straight into the ocean, and then the fishing recently rebounded just as the new sewer system was coming online. I wanted to see if these two events were correlated, or just coincidental, so I reached out to Ross Boucek, Florida Keys initiative manager for the Bonefish & Tarpon Trust (bonefishtarpontrust.org).

“We funded an intensive study to look at long-term trends of bonefish to determine what environmental factors could have been responsible for the decline,” said Boucek. “Results suggested it was not any one factor, but many interacting factors—including water quality—that led to the demise of bonefish in the Florida Keys.

“The conversion from septic to a contained municipal sewer system was a great conservation victory, and we have seen improvements in specific areas where that pollution was impacting our fish, wildlife, and habitats,” said Boucek. But he says local sewage is just the tip of the iceberg. The biggest source of pollution is residential and agricultural pollutants coming from the mainland.

“In the Keys, we have a new era of water quality issues,” said Boucek. “Exponentially growing populations on the mainland are pumping more pollution into estuaries upcurrent of the Keys. These sources of pollution are more distant, but reach the Keys with favorable ocean currents. King tides are becoming more pronounced and tropical storms are more frequent and more intense, inundating urban areas and flushing pollution from roads, lawns, and other sources into the ocean.”

New Recruits

Boucek says those large bonefish spawned in the early 1990s died of old age, and for more than a decade the Keys weren’t getting any new bonefish recruitment.

“There are a couple reasons why we stopped getting new bonefish,” said Boucek. “First, our larval supply chain could have been disrupted. In the early 2000s, BTT put a lot of effort into catching larval bonefish in the Keys. After soaking many larval traps, we only captured a total of nine larval bonefish. When we set those same traps in the Bahamas we get hundreds of larvae in each trap every time. The lack of larvae could either be from a lack of spawning fish in Florida, or from changes in the ocean currents that prevented larvae spawned in Belize, Mexico, or Cuba from getting to the Keys as in previous decades.

“Juvenile fish are also very hard to keep alive. If the structure isn’t there, or the water quality is bad, then they won’t survive. BTT has funded three different studies to find juvenile bonefish in Florida. The only place we seem to catch them is in Garfield Bight in Florida Bay, and that’s the epicenter of a 60,000-acre seagrass die-off. There is reason to believe that juvenile habitat degradation was, and still is, playing a role keeping our bonefish population from reaching its potential.”

Despite all that, Boucek agrees that since 2014, new bonefish are appearing on Florida Keys flats.

“Starting in 2014, a new wave of babies came in, followed by two more new generations in 2015 and 2016,” said Boucek. “The size classes are approximately 15 to 18 inches (2016 fish), 18 to 20 inches (2015 fish), and 22 to 25 inches (2014 fish). Although these new fish are encouraging, we don’t know where they came from, or if more new fish will continue to enter the Keys population.

“Bonefish have a very unique way of reproducing. They are island fish, and use their larvae to colonize or repopulate other islands that may have been decimated by a hurricane. When bonefish spawn, they migrate from places as far as 70 miles away to a specific site. There, they form aggregations that can exceed 10,000 bonefish. In the evenings, those fish swim to blue water, dive to depths greater than 200 feet, and deposit their larvae in ocean currents like the Gulf Stream. Their larvae can live in these currents for up to 70 days before they need to settle. This unique way of reproducing is why we have bonefish in crazy places like Christmas Island.

“From an evolutionary angle, this is a great strategy to keep the species going. However, from a conservation perspective, to keep any one bonefish population thriving means making sure all those other neighboring populations that supply larvae are healthy.

“Once our bonefish population started to decline in the Keys, and we learned about how they reproduce, we conducted a genetic study on Keys bonefish. We learned that a significant percentage of Florida Keys bonefish are spawned in places like Mexico and Belize. Learning this, we established a long-term conservation hub in that region to reduce commercial harvest of the species and protect the habitats that support them. Bonefish are designated as catch-and-release only in Belize, and we hope Mexico follows suit. The bonefish decline in the Keys is likely a result of many small stresses that added up. This is one of the stresses that we are working hard to heal.”

After speaking with Boucek it became clear that the municipal sewage treatment in the Keys is just one small part of the equation, but there is hope for the future as healthy bonefish populations in foreign waters continue to use the Gulf Stream to seed our waters, and it seems that the spawning events and the currents have been favorable the past few years. It’s amazing to me that these fish end up on our flats at all, but as Dr. Malcolm says in Jurassic Park: “Life, uh, finds a way.”

Bruce Chard has been a Florida Keys guide for more than 25 years. He is a frequent contributor to Fly Fisherman. His previous stories include “Tarpon Caviar,” the cover story of the June-July 2016 issue, and “Inherit the Salt” in the June-July 2018 issue.