SAUSALITO (KPIX 5) — The waters of San Francisco Bay are cloudy from the storm that blew through the Bay Area but the it runs much deeper than just muddy water.

The John Dillard is one of two highly specialized boats equipped with cranes that are trying to keep the shipping lanes clear of debris. It’s a big job.

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Kixon Meyer is a boat captain for the Army Corps of Engineers.

“Everything that’s in this pile and that pile over there came off the John Dillard in the last two weeks,” he says pointing to 2 huge piles of debris.

A huge pile of giant trees is getting larger by the day, all washed down into the bay by the flooding.

Meyer points to where a giant log was hit several times by an unknown boat before he and his team could pull it from the bay.

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“There was definitely prop contact, propeller from a boat contact right here, and maybe right here,” he points out. “Our biggest concerns are the ferries that travel about 30 knots with about 300 people on board.”

While ferry captains are on high alert for debris, they travel before dawn and after dark so avoiding it can be hard.

When a ferry accidentally hits a submerged log, its giant propellers are badly damaged. That just happened to a boat recently.

“Went into dry dock Saturday evening and hopefully it will be back in a couple days,” says Jim Swindler, a Golden Gate Ferry Deputy General Manager. “We had to put two brand new propellers on it.”

It’s not just giant trees and logs the Corp of Engineers is finding out in the bay. There’s a lot of unbelievable stuff out there too. Tires, old boats and pilings with steel spikes are especially dangerous for passing vessels. They found a Jacuzzi once and have picked up several cars.

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“We get a lot refrigerators,” says Meyer. “Most of them still have food in them!”