Lain Goodwin eased his boat into Florida Bay, hoping for the water to clear. He looked for the holes in the bay floor where he would always catch some snook, but there was nothing to see. The only clear blue was the sky.

Back east across Blackwater Sound, under the construction along U.S. 1, through Barnes Sound and 5 miles north into Biscayne Bay, the water remained the same deep green as the mangrove stands that hug the islands of the upper Florida Keys.

The shallow waters from Key Largo north to Arsenicker Keys have been clouded by a blue-green algae bloom spreading across 175 square miles of Florida and Biscayne bays since autumn. The bloom stretches into portions of Everglades and Biscayne national parks, threatening the fragile seagrass that supports the state’s fishing industry, conservationists say.

“I just don’t see an end to it,” Goodwin said Thursday aboard his 22-foot fishing boat, idling in the calm yet murky waters off Homestead where the bay is only 8 feet deep.

Disturbances from last year’s hurricanes likely stirred up phosphorus in the water, feeding the algae, but construction widening an 18-mile stretch of U.S. 1 between Florida City and Key Largo may also be to blame, according to a South Florida Water Management District analysis released late last month.

“An interaction of these two factors (disturbance from road construction plus hurricanes) appears to be the likely cause of the blooms,” the report states.

The road widening and bridge construction began in April 2005 after a federal judge denied an attempt by environmental groups to block it. The $268 million project, which the groups said did not meet state and federal environmental standards, is scheduled for completion by June 2009. The road is the main route connecting the Keys and mainland Florida.

Florida Department of Transportation officials dispute the water management district’s analysis of the bloom, calling the report preliminary.

Two activities cited in the report — the mulching of mangrove trees and mixing fresh mulch into the soil — have already stopped, and there is no evidence either was harmful to the environment, district transportation officials said Friday.

“If construction did contribute, I would think it would be very little. I think nature is the biggest culprit,” said John Martinez, a district secretary.

The algae is concentrated near the road construction in waters where such a bloom has never been recorded, according to the water management district report.

“It’s where the water looks the worst, and it’s persistently in place around this road construction,” said Peter Frezza, research coordinator at the Audubon of Florida’s Tavernier Science Center.

The conservation advocacy organization has asked the water management district to limit or halt the road work until a cause and remedy for the bloom is found.

Audubon has been studying the effects of water quality on seagrass, fish and birds in Florida Bay. Frezza said current light penetration readings in the bay are the dimmest on record.

Storm surge alone could have disrupted the sediment and released excess nutrients into the water, Frezza said, “but here’s the problem: We’re almost a year off that hurricane season and this bloom has not subsided at all. If anything, it’s getting worse.”

Seagrass holds down the sediment in the shallow bay waters, but needs sunlight to thrive. The algae bloom, though nontoxic, chokes off the plants’ light source.

“If we start having mass seagrass fatality, it could be a disaster for the Florida Bay. That’s the bottom of the food chain, everything is based on seagrass — from the tiny little bacteria and the small crustaceans that eat them, and it goes all the way up to the largest fish,” Frezza said.

A group of potential kayakers walked out of Florida Bay Outfitters in Key Largo after a recent glimpse at the green bay waters that seem to swallow the slender legs of white egrets, said owner and kayak guide Frank Woll. “It’s kind of depressing,” said Woll, who encourages his customers to paddle in the ocean instead. “It’s been around since the storms, and it hasn’t gone away, which is not normal.”

Goodwin and other boat captains say the bloom has disrupted their fishing charters out of Key Largo.

Goodwin takes nearly all his charters — he sheepishly hands over a business card for his Dirty Waters Charters, saying, “It’s not so funny now” — into eastern Florida Bay and the southern end of Biscayne Bay.

“Normally it looks like an aquarium,” he said. “The fishing, it’s been dead here. I gave it up three or four months ago.”

Gag grouper did not return to the shallow waters this spring, eliminating one of his specialty trips. Lobster catches would probably have to be replaced with night fishing trips farther west in Florida Bay, he said.

He spends an extra $10 to $30 a day on gas for his boat now, trying to out-race the bloom and find clear water, he said.

“I can shoulder the loss of money if this is just temporary, but if we’re talking about 10 to 20 years, then we’ve got some major issues,” Goodwin said.

Seagrass beds farther west in Florida Bay still have not completely recovered from an algae bloom more than a decade ago, Frezza said. Negligent and inexperienced boaters have also cut wide swaths across seagrass beds in the bay, destroying fish habitat, conservationists have said.

“It could probably become a really dirty basin, and realistically we could never see seagrass in the bay again,” Frezza said.

On the Net:

Audubon of Florida: http://www.audubonofflorida.org/index.html

Florida Department of Transportation: http://www.dot.state.fl.us