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SAN FRANCISCO BAY — A lookout on the patrol boat spots a floating hazard three miles from the Golden Gate Bridge and shouts over the roaring engine. “There! It’s a three birder!”

The crew of the John A. B. Dillard swings into action.

Capt. Kixon Meyer deftly pulls the 100-foot boat up to and aside a broken piece of pier with long metal spikes capable of puncturing hulls or choking propellers of vessels plying some of the busiest waters along the West Coast.

The boat crane operator uses giant pincers to grab the timber and drop it into a debris box on deck.

Log by log, timber by timber, the Army Corps of Engineers vessel is making San Francisco Bay and Delta boating waters safer in a year of torrential storms that have dramatically increased the number of dangerous objects in the water.

High flows in and on rivers, creeks, bays, forests and meadows have ripped loose and swept downstream trees, piers, boats, rudders, refrigerators and other flotsam and jetsam.

“This is a banner year for our work,” Meyer said. “Take that one we call a three birder because it’s big enough for three birds to perch on it. We don’t go after plastic cups. We go after the big stuff that could damage a boat with 300 people.”

The Dillard collected six tons a day of debris the past two years, but it averaged about 17 or 18 tons per day in January and February.

On some days this winter, the boat wrangled in nearly 50 tons, filling the deck end to end with giant junk.

Several refrigerators, two cars and a 4-foot-plus diameter eucalyptus tree so heavy it had to be towed to shore, were rounded up and loaded into a salvage yard in Sausalito near the docks for the Dillard and its sister boat, the Raccoon.

“They are unsung heroes of San Francisco Bay,” said Ernest Sanchez, spokesman for the Water Emergency Transportation Authority, which carries 2.7 million ferry passengers a year across the bay. “They are critical to the operation of the ferries. They call it debris, but it can be monster debris.”

Floating objects damaged propellers of two ferries this winter. Two other ferries were damaged when their water jets sucked in debris, causing expensive repairs, Sanchez said.

A wartime tragedy in 1942 led to the creation of debris-salvage patrols. Adm. Chester Nimitz, the commander of the U.S. Navy’s Pacific Fleet, was in a seaplane that crashed into debris in the bay that ripped open its bottom. Nimitz, the namesake for the Nimitz Freeway in the East Bay, was injured, and his pilot was killed.

Alarmed government officials tapped the Corps of Engineers, an Army branch better known for building dams and regulating waterways, for the job.

In 2013, during the America’s Cup races, both the Dillard and Raccoon worked each day to make certain no hazard sliced or upended super light racing yachts that zipped along at speeds of 40 mph or more.

San Francisco Bay’s geography makes it a natural gathering place for floating hazards.

The bay is like a giant 400-square-mile bath tub with a narrow outlet, the Golden Gate, less than two miles long. But water runoff into the bay comes off 40 percent of California’s land mass, including thousands of miles of rivers, creeks, sloughs and streams.

“Some debris makes it out to the ocean on its own,” Meyer said. “But if we don’t pick up the big stuff, there is a fair chance it will just slosh back and forth inside the bay, and remain a hazard.”

Finding the hazards is no easy task at times.

“We follow the tides,” said Meyer, an Orinda resident and longtime seaman who joined the Coast Guard at age 19 and has traveled many oceans since then. “You look for the areas where the incoming and outgoing waters collide, and that’s where stuff gets trapped.”

Tips also pay big dividends. The crews get tips radioed or phoned in from the Coast Guard, ferry boat crews, harbor masters, kayakers and other boaters. “They call it in,” he said. “We pick it up.”

The flotsam, though, can float away. On a recent trip, the Dillard cruised to Larkspur to check out a Coast Guard report from the night before of a 40-foot-long log with tules dangling off. It was gone when the Dillard arrived.

So the boat cruised to a San Francisco pier and later the Berkeley Marina, where many logs and floating lumber were waiting, tied up along docks for the crews to pick up.

“In a year like this, I would hate to think of the danger to boats in our harbor if (the Corps boats) weren’t here to get this stuff,” said Brian Gavin, the acting Berkeley harbormaster.

Collecting the debris can be a struggle. The crew sometimes has to saw heavy trees into pieces before lifting it aboard. Other times, they have used wire cutters and poles to loosen debris wrapped around bridges.

The captain calls in hard cut construction divers to investigate beams or logs sticking above the surface that are sometimes stuck to the bottom of the bay.

Meyer acknowledged that some of the appeal of the job is spending long hours on the water, a place he likes to work and vacation.

From the bridge of the Dillard, Meyer looked out four big glass windows in the bridge to see vast expanses of water and seals rolling in the water. A few kayakers paddled nearby.

“I had a desk job for a while, but I decided I wanted to go back to the water,” he said. “We work on the water, and we help make it cleaner and safer.”