A massive effort to clean up San Diego Bay has become its own big mess.

The clean-up was supposed to get under way last week — instead, the city and a major local company are pointing fingers about who’s at fault.

In March 2012, the regional water quality control board, a sub-agency of the state Environmental Protection Agency, issued an order to a list of private companies and public entities to begin cleaning up decades’ worth of pollution that had seeped into the San Diego Bay.

The city of San Diego, the San Diego Unified Port District, the U.S. Navy, San Diego Gas and Electric and two of the largest shipbuilding companies operating on the bay were all ordered to pay into the $75 million clean-up effort.

Ever since, the parties have been squabbling over who should pay what share of the costs of dredging up waste that’s accumulated on the bay floor.

“The contaminated marine sediment has caused conditions of pollution, contamination or nuisance in San Diego Bay that adversely affect aquatic life, aquatic dependent wildlife, and human health” in the bay, the order reads.

All parties have reached a settlement over their share of the clean-up, except the city of San Diego, which is suing NASSCO, a shipbuilding company located in front of the area scheduled for clean-up, in federal court over how much it owes the clean-up effort. The suit isn’t scheduled to go before a judge until 2015.

Last week the port and NASSCO reached a tentative agreement settling the port’s share of the clean-up costs. That appeared to pave the way to start the dredging, but the city of San Diego and the shipbuilder’s disagreement is still holding things up.

Meanwhile, the mandated start date for clean-up efforts, per the regional water board’s initial order, came and went last week.

That led David Gibson, the regional board’s executive officer, to fire off a harshly worded letter to all of the responsible parties demanding they inform him by Sept. 25 – Wednesday – of their plans to comply with the clean-up order.

“We’ve already informed them that they’re informally in violation of the order,” Gibson said.

If the parties don’t respond, or if he isn’t satisfied with the responses, Gibson will issue a formal notice of violation.

A violation order would include penalties for missing the deadline, he said.

“The board means business with this clean-up, and I would not want to test their patience in this case,” he said. “If we send out violation it’ll be in earnest, not paperwork.”

On Tuesday, the City Council voted on a resolution it hoped would appease Gibson.

The resolution sets aside $6.5 million in a public trust, to be drawn down as NASSCO invoices the city for its share of the clean-up, but would allow the city to continue its lawsuit against NASSCO to lower or negate its obligation.

NASSCO opposed the resolution because it’d still be on the hook for the ongoing costs of fighting the lawsuit, and asked that the city simply settle the suit outright.

Gibson said he hadn’t yet received word the clean-up was imminent, but all of the parties have individually assured him they support the clean-up order.

Whether the city’s resolution will stop any penalties is unclear.

He said he’s still optimistic the clean-up will begin within the next month.

“They should have been well-positioned by now to comply with the board’s order,” he said. “That they didn’t is very concerning. We now expect them to fund at least starting point of clean-up and work out details over next three years as they execute the clean-up.”

Deputy City Attorney Fritz Ortlieb said at Tuesday’s Council meeting that NASSCO’s refusal to start the clean-up without a settlement – despite the city setting up the $6.5 million trust – proves the shipbuilder is the one really holding up the process.

“There is no reason in the world that this work cannot commence, except for NASSCO’s choice to demand the settlement of the litigation in connection with this,” Ortlieb said.

Jill Witkowski, the “waterkeeper” for San Diego Coastkeeper, a nonprofit that advocates for healthy water in the region, put the continued delay on the city’s shoulders, and said she wished the City Council would have urged the city attorney to settle.

“It’s disappointing that it’s a municipality holding it up,” she said. “We deserve better.”

The regional board’s clean-up order doesn’t force the effort to be completed until more than three years from now, but one reason the late start is troublesome is because the dredging can only take place from September through March.

The rest of the year is the nesting season for the California Least Tern, a migratory bird listed as an endangered species.

So the clean-up really has three dredging seasons available before it reaches its deadline, and we’re already two weeks into one of them.

Andrew Keatts

I'm Andrew Keatts, a managing editor for projects and investigations at Voice of San Diego. Please contact me if you'd like at andrew.keatts@voiceofsandiego.org...

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