Veteran Islamorada flats guide captain Craig Brewer used to keep very busy throughout the autumn months leading anglers to the catch and release of multiple bonefish in a day’s outing on Florida Bay. For most of his 25-year career, Brewer could count on those fall bonefish trips for a good percentage of his income. Not anymore.

“A lot of places where we used to find them, they’ve left,” Brewer said. “They’re just not around anymore. I lost a lot of days because of that. The ‘sportfishing capital of the world’ is not here as far as bonefish are concerned.”

Instead, said Brewer and some of his fellow guides, they must run north to Biscayne Bay or south to the lower Keys to locate bones for their clients. Or, if they stay in Florida Bay, they opt to chase redfish or snook.

“There’s definitely less and less bonefish in the area,” said Islamorada guide captain Dave Denkert. “Only a few flats hold fish and everybody’s fishing them.”

Nearly everyone agrees that the Florida Bay bonefishery has been in decline for a very long time, but took a steep dive in the past five years. A study published early this year by University of Miami bonefish researcher Mike Larkin and colleagues found the bonefish stock from Biscayne Bay through Key West is “bordering on an overfished status.” The last bonefish census in the region conducted in the fall of 2010 by UM and the non-profit Bonefish Tarpon Trust found a “substantial decrease” since guides and anglers began the annual count in 2003.

Researchers, guides and anglers cite a host of possible reasons for the scarcity of one of the South Florida’s most important sport fish: deteriorating water quality (algae blooms and septic system leaks); loss of sea grass and other habitat and prey; boating and fishing pressure; the extended cold snap of 2010; catch-and-release mortality; commercial netting that took place decades ago — and the combination of all of the above.

“It’s tough to take corrective action if you don’t know what the problem is,” said fisheries scientist Aaron Adams, operations director for Bonefish Tarpon Trust, a non-profit organization dedicated to research and advocacy for shallow-water sport fish.

BTT and UM have shifted efforts away from tagging and counting bonefish to finding out why their numbers are way down and why they frequent some locations while shunning their past haunts.

Adams said BTT has commissioned a study by Audubon Florida to determine if prey species (crabs, shrimp, and worms), sea grass, and water quality in the formerly bonefish-rich flats of Florida Bay have declined over the past 30 years.

Audubon researcher Pete Frezza says he and his colleagues will compare data from previous studies conducted in the 1980s and ’90s on abundance of animals and sea grass in several flats that once were inhabited by bonefish — Cross Bank, Buchanan Bank and Nine Mile Bank — to what lives there now. Then they’ll compare that critter coverage to two control areas where bonefish currently roam — Sands Cut in Biscayne Bay and the Sawyer Keys in the lower Keys.

Frezza says the field work — using metal boxes to collect bottom samples and seine nets to sift through them — is pretty much done. He expects to publish the findings around the first of the year.

Frezza, who also works as a bonefish guide in the Keys, says the study won’t bring the fish back but may determine why they aren’t hanging out where they used to be.

“Food and being safe are the primary things that drive these fishes’ lives,” Frezza said. “These are fish of strong, clear, ocean water tides. Florida Bay was an estuary — marginal as habitat. They were willing to go out of their comfort zone because there was food. Now there may not be tons of food.”

Captain Rusty Albury, a sixth-generation Islamorada native and 26-year veteran flats guide, says he has noticed a lot more pinfish on the flats of Florida Bay since the 2010 cold kill. Pinfish, which extend north to mid-Atlantic waters, are more tolerant of cold than some baitfish species.

“The pinfish are competing with the bonefish on the flats,” Albury said. “Why they’re not competing with them in Biscayne Bay, I don’t know.”

Guides say the lack of bonefish in the Islamorada area is hurting the local economy. Adams of BTT doesn’t doubt it; his organization has commissioned the first economic impact study of flats fishing in the Keys, due for completion in mid-2013.

Said Adams: “If water coming out of the Everglades is the problem, for example, the economic impact of the fishery would provide leverage to get that fixed.”