To do a riff on Mark Twain: recent reports of the Gulf of Mexico’s recovery have been greatly exaggerated.

Yes, as the media relentlessly tell us, the Gulf, at least on the surface, looks pretty normal, surprisingly so in the wake of this year’s BP deepwater drilling disaster and lesser insults like the September 2 Mariner Energy oil platform fire.

Shrimping and oystering have resumed somewhat (though many still need to pursue claims for business perhaps lost forever). And seabirds and human sun-worshippers, neither group with any visible oil coverage, still congregate on gorgeous sandy beaches. A loose journalistic consensus, fueled as usual by corporate influence, has gelled: all is well – or will soon be, thanks to Mother Nature’s inscrutable bacterial clean-up efforts. After all, petroleum is a naturally-occurring substance, right (not to mention oil-consuming microbes)? And underwater oil seeps have been observed in the Gulf since time immemorial.

But several stakes – in the hands of various powerful “stakeholders” – still pierce the heart of this unparalleled subtropical marine ecosystem. And perhaps the most serious one has been hiding in plain sight for decades.

Specifically, the Gulf is an oceanic hostage to a terrestrial threat that dominates the “heartland” of the Lower Forty-eight: modern industrialized agriculture. And if ever there was an ecological wolf in sheep’s clothing, this is it: “conventional” farms throughout the vast Mississippi-Missouri-Ohio basin produce nitrogen and phosphorus runoff on a massive scale that creates a Gulf “dead zone” depleted of oxygen and inimical to aquatic life.

All things considered, this runoff may do more harm to the Gulf’s marine and riparian ecosystems than almost anything BP might dream up. But we need to be more specific. It’s not farming per se that’s the problem. It’s synthetic fertilizer and other chemical runoff that, having been applied in excess to cornfields and other cultivated areas, is annually washed off “conventionally” cultivated soils upstream – with the rich, or formerly rich soils themselves disappearing into the toxic soup. The mechanism of destruction is simple: The chemical runoff fuels the growth of excessive algae which then dies and decomposes, robbing the seawater of oxygen and creating so-called “hypoxic” zones commonly described as “the size of New Jersey” or Delaware or  perhaps larger states as time goes on.

This perverse process, which tends to be concentrated with the start of the growing season, is also expensive. A 2006 study by the Washington-based Environmental Working Group determined that runoff from the greater Mississippi Basin, at a rate of 7.8 million pounds per day in the springtime, accounted for 70 percent of the nitrate pollution in the Gulf (by contrast, municipal runoff accounted for just 11 percent.) and ran up a bill of $400 million a year.