The area around the Sebastian Inlet, long renowned as a fishing location attracting anglers from across the state and nation, had an unusually small catch this past winter and scientists blame brown algae fed by sewage leaking from septic tanks.

"It wasn't good all winter long," said light-tackle charter boat captain Glyn Austin. "Typically, we catch a lot of jacks and a lot of bluefish, pompano and flounder in the inlet, but many times you'd go in there and it was dead."

Inshore fisherman Tom Pierce recalled murky water with 8-inch visibility he encountered in the Indian River Lagoon near the inlet. The coffee-colored flats were clotted with algae, making it impossible to see schools of spotted sea trout that normally roam the seagrass beds in the area.

After casting a range of lures for two hours without a bite, Pierce and his companion motored south to Vero Beach where they found clearer water and a handful of keeper trout.

"Fishing is tough as hell anymore," Pierce said. "It's consistently more difficult, with fewer numbers of fish."

Fed by Irma's flooding rains mixed with discharges from leaky septic tanks and broken sewer pipes, the organism with the scientific name of aureoumbra lagunensis bloomed in the lagoon last winter for the third time since 2012. Though not toxic to humans, the 'brown tide' smothers sea grass, suffocates fish, and overwhelms oysters and clams that normally filter the brackish waters.

By early June, most of the brown algae that bloomed from Brevard County's Banana River south to Vero Beach in the wake of Irma had dissipated and the fishing had improved – but maybe not for long.

Now that the rainy season is here, bringing deluges that wash contaminants into the lagoon, the stage is set for a recurrence of the brown tide, according to Dr. Brian LaPointe, a research professor at Florida Atlantic University's Harbor Branch Oceanographic Institute who has studied the lagoon for 40 years.

"It's unlikely it's going to go away until we cut off its food," LaPointe said.

LaPointe and colleagues conducted a multi-year study of the entire 156-mile lagoon, which passes through five counties. The researchers measured high nitrogen loads in the algae-laden water samples they collected and "fingerprinted" them, LaPointe said.  The primary source of the algae producing nitrogen:  not lawn or agricultural fertilizers, but human waste.

"This is a sewage problem," LaPointe said.

One of the bloom's hot spots last year occurred in Vero Beach's Bethel Creek after a broken sewer line along Highway A1A spilled 3 million gallons of waste into the lagoon.

LaPointe says the key to cleaning up the ecologically sensitive estuary is to lower the concentration of nitrogen, and with 1.6 million people now living in the watershed, current measures aren't working.              

"We need not just sewage treatment, not just getting rid of septic tanks and leaky pipes.  We need advanced waste treatment," he said. "New sewage treatment plants achieve 95 percent nitrogen removal.  Once you cut off the source of the nitrogen, the water clears up, the sunlight hits the bottom and the muck goes away."      

Vero Beach Water and Sewer Director Rob Bolton said the city is doing what it can. Vero doesn't have an advanced sewage treatment system to eliminate or reduce nitrogen to three parts per million or less, but its system does lower the load to about 12 parts per million, he said. Treated wastewater is sent into a deep injection well instead of being discharged into the lagoon. 

Other city measures include discouraging homeowners from fertilizing during the rainy summer months and a septic-to-sewer program that aims to eliminate septic tanks within the city limits. In beleaguered Bethel Creek, the city is working with the Ocean Research and Conservation Association (ORCA) to install an aeration system, create fish nurseries and restore the shoreline.

City Councilman Tony Young believes there is growing sentiment to adopt a stormwater utility fee to pay for projects to clean up the lagoon.

"We need to support measures to rectify the damage that's been done by the increase in population," he said. 

Indian River Lagoon Council executive director Dr. Duane DeFreese says everyone is watching the lagoon closely to see what this summer will bring.

"In Sebastian and Vero, the water quality looks pretty good right now," DeFreese said. "That doesn't mean that in three days from now we won't see something pop up.”