Water from the Delta has been fought over for more than a half century. Reporter Lauren Sommer sat down with Barry Nelson, the Senior Policy Analyst for the Natural Resources Defense Council to discuss the future of the Delta and California’s water supply.

For another viewpoint, check out this Q&A with Jason Peltier of the Westlands Water District or see the rest of our series coverage.

Barry Nelson, Senior Policy Analyst with the Natural Resources Defense Council.

When were the first signs that the Delta ecosystem was in trouble?

Since the 1960s, we’ve seen a steadily growing trend of diversions from the Delta. If you look at long-term averages, you filter out the impacts of droughts and wet years, we’ve taken more and more and more water from the Delta pretty steadily for the last 50 years, and that really hit a crisis point in the ‘90s. That’s the point at which we started seeing the winter-run salmon and the Delta smelt being protected under the state and federal Endangered Species Act.

And ten years ago, things really changed dramatically. Starting in 2000, suddenly we started taking a lot more water out of the Delta for a lot of reasons. It was an enormous increase, about a 20% increase on average. And the ecosystem crashed. It was called the “pelagic organism decline.” But what it meant was pretty simple: that everything swimming in the Delta was in deep trouble.

So now we’ve got half a dozen species in deep trouble in the estuary and a fishing industry that’s honestly fighting for survival.

What caused their decline?

A lot of work has been done looking at this catastrophic, across-the-board, collapse of the Bay Delta ecosystem. And the bottom line was recognition that, while there are lots of stressors, there are pollution problems in the ecosystem. We do have invasive species like clams that have come from overseas. But the core problem is the amount of water we pump out of that system.

There was a huge fight in the courts over this issue. And ultimately, the courts and then the agencies imposed a new set of rules that really have returned us to the level of pumping we saw for about 30 years prior to the 2000’s.

And what were those rules on pumping?

The Delta’s a complicated ecosystem. As water flows through it, it flows through it in a complicated pattern. Fish have evolved to survive with that pattern; water coming through at certain times of year, and flowing through those Delta channels into the Bay.

Basically, the federal rules control two things: the amount of water that flows all the way through the ecosystem into the Bay in order to maintain a healthy ecosystem and the extent to which some of the channels within the Delta flow backwards.

The pumps in the south Delta are so powerful that they literally reverse the direction of flow in these Delta channels. And if you’re a young migrating salmon swimming downstream towards the ocean as Mother Nature programmed you, when the Delta channels are flowing the wrong direction, it’s very easy for those fish to follow that water and get sucked right into the pumps. And that’s why those pumps have killed in the last decade or so not a million fish, not tens of millions of fish, but over a hundred million young fish killed just at the pumps.

So if you could design your ideal plan for the Delta, what would that look like?

First, we know we need to see some real habitat restoration in the Delta. We’ve converted almost every scrap of habitat in the Delta to farmland, and in order to restore a healthy Delta, we need to return some of that to habitat. And actually I think that’s something where there’s a fair amount of agreement. How you do that is not trivial, but I think there’s a fair amount of agreement around that. And given the challenge of maintaining all of the existing levees in perpetuity, the question is: are we going to do it in a planned and thoughtful way?

Second, we really don’t have a choice but to maintain a lot of our Delta levees for a couple of decades. It’s going to take a long time to make major changes in the Delta. And there is so much infrastructure, the Delta communities, Delta farming, and water supply that depend on Delta levees today.

Third, from our perspective, the challenge we face in terms of exporting water from the Delta is first figuring out how much water we can safely pump from the Delta. And then designing a facility around that.

You’re talking about the “peripheral canal,” right? A canal or tunnel that would take water around the Delta?

Well, there are two conflicting visions for a facility in the Delta. One is the old plan. Fifty years ago, the state of California was planning to build a peripheral canal around the Delta, an enormous facility that would allow those pumps in the south Delta to take water from the north Delta and pump it around the Delta rather than through Delta channels. And that was really a simple proposal to simply take more water from the ecosystem. We know now that that, the amount of water that that would have taken would have been devastating to the ecosystem.

That’s the old version of the canal. But there’s a new version out there. And that is a proposal to deal with earthquake risks in the Delta. It’s to deal with the fact that there really are earthquake risks in the Delta that represent significant threats to water supply. And a facility could provide a lifeline in case the Delta was to temporarily fail. What we’re struggling with right now is that we have competing interests in California advancing two different visions for what the problem is in the Delta.

With such a long history of disagreement, what are the chances of agreeing on a plan?

There’s a reason that the discussion on the Delta is so politically heated that people don’t usually talk about. And that is California is out of rivers. If you look around the state of California at the Colorado River and the Klamath River and the Trinity River, the Owens River, the San Joaquin, on and on, we’ve really started to hit real hard physical limits in the amount of water we can take out of all of those rivers.

Ten years ago we weren’t paying enough attention to sea level rise impacts. We weren’t really thinking about earthquake risks in, in the Delta. So there really is a sense that we need to figure this problem out this time.

That’s what makes the Delta debate so compelling. The Delta is an incredibly important ecosystem. It’s an incredibly important place for a quarter million people who live there. And it’s a tremendously important water supply for the state of California. There are a lot of reasons why our planning efforts today could fail, but it’s so important to the future of the state. It’s so important to the health of the Bay and the Bay Area, it’s so important to the future of the salmon industry, to the residents of the Delta. We can’t let that effort fail.

UPDATE on 10/23/09: From the San Francisco Chronicle – "Two World War II cargo ships moored among Benicia's fabled "ghost fleet" since the late 1940s will be towed out of Suisun Bay next month, scrubbed clean in dry dock and ultimately sent to Texas to be broken up and sold for scrap".

Read more about the clean-up effort in the Chronicle here.

On the surface of the story, the Ghost Fleet of Suisun Bay (commonly called the "Mothball Fleet" but most accurately referred to as the Suisun Bay National Defense Reserve Fleet) is leaking toxic waste in the form of peeling ship paint containing nasty heavy metals into an already stressed bay ecosystem. Bad guys: Mothball Fleet. Good guys: Enviros who are suing. Simple, right?

But when we began digging into the story, we found the origins of the problem and current impasse to be a bit more convoluted. I'll attempt to quickly summarize: The fleet has been there since the 1940's. It wasn't until 2006 that it came to light that the exterior paint is peeling from the ships and falling into the bay. Many tons of toxic heavy metals have already fallen into Suisun Bay and there's a lot more to be had. Oddly enough, the story was initially triggered by a study that was commissioned by the federal body who oversees the fleet, the Department of Transportation's Maritime Administration, or MARAD for short. So the Contra Costa Times got a hold of a draft of that report and now, the ships are at the center of a different kind of battle long after they've been decommissioned.

Environmental groups (NRDC, Arc Ecology and San Francisco Bay Keeper), community leaders and water regulators justifiably want MARAD to either remove or better maintain the ships so that they are not polluting these waters that serve as both fishing and nursery grounds for several fragile or threatened species. That includes humans who are often out there catching fish for dinner. Historically, MARAD has been regularly removing and dismantling the ships but like most federal bodies whose charter was drafted during WWII, alacrity is not at the top of their mission statement.

View Suisun Bay's Mothball Fleet in a larger map

The real issue now seems to be that MARAD has had to completely stop removing ships because they can't clean their hulls of potentially hazardous invasive biological species (to comply with the U.S. Coast Guard's National Aquatic Invasive Species Act of 2003) without scraping more paint into the bay. So, until someone develops a system to clean the hulls that doesn't scrape more paint into the water, the San Francisco Regional Water Quality Control Board says that MARAD can't remove the ships.

The one possible solution that everyone pretty much agrees upon is to dismantle the ships locally so that they don’t have to be cleaned of invasive species. There are currently no ship dismantlers operating on the West Coast but there's a company called Allied Defense Recycling located on Vallejo's Mare Island Naval Shipyard that's chomping at the bit to tear those ships apart. But they've also run into red tape. And while they await permits and approvals from multiple parties, the ships continue to rot and pollute.

It's always easier to write a story with clear heroes and villains. But to me, it does seem that MARAD, environmental groups and water regulators all agree that we have a problem that must be addressed. So, what now? I guess we wait. Perhaps this lawsuit will kick start some aspect of the clean-up process but in the meantime, frustration mounts for all parties involved and many pointing index fingers are suffering from overuse.

Watch the "Ghost Fleet" TV Story online, as well as find additional links and resources. Also, check out the online photo set of the ships and behind the scenes images.

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You may listen to the "Cement – A Dirty Business" Radio report online, as well as find additional links and resources. Also don't miss our behind-the-scenes photos for this story.

Amy Standen is a Reporter for QUEST and Radio News at KQED-FM.