The closure is the latest chapter in the city's years-long struggle to tame the Gowanus, which is located in between two gentrifying brownstone neighborhoods. The mile-and-a-half Gowanus starts in New York Harbor in Red Hook and dead-ends north into Boerum Hill. But since it only has one outlet, water doesn't circulate and sediment, especially from neighboring industrial businesses, just accumulates at an estimated rate of half a foot a year.

In 1999, the Giuliani administration reopened the underground tunnel, which was built in 1911, in order to bring water from another part of New York Harbor, just opposite Governors Island, into the Gowanus. But that solution, while an improvement, proved insufficient for the fetid waters of the canal and the sewage outflows that pour into it after heavy rains.

"The tunnel is a century old and needs to be repaired and expanded," said Carter Stickland, the deputy commissioner of the city's Department of Environmental Protection (DEP). "It has a limited capacity, only has a single pump, and we need to shut it down for several weeks a year for repairs."

While the tunnel is out of commission--for the next 26 months--the DEP will drain the tunnel, replace its single old pump with three new ones, and construct a mile-long pipe at the canal head in Boreum Hill that will bring sewage directly to the Red Hook Wastewater Treatment Plant.

But 26 months is a long time, representing two, maybe even three summers. In order to mitigate the effects of closing the flushing tunnel, the DEP today also switched on a $9 million aeration system--think of it as a pump for a very large fish tank--that takes water out of the canal, suffuses it with supersaturated oxygen, and then dumps it back into the canal. That's supposed to cut down on odors, though it won't do anything for sediment build-up or other sorts of pollution.

That system alone will cost $2 million to operate over the next two years and uses oxygen that is generated at the DEP's facility from the surrounding air.

Neighbors like Marlene Donnelly, who lives a block away and is a member of Friends of the Greater Gowanus, are crossing their fingers that the oxygenation system will work.

"We are hopeful that this fix, actually from what we have heard, will work for our community, will be livable and the odors will be manageable," Donnelly said, "because a summer with 100 degree heat and no circulation could be pretty deadly down in the area."

The improvements to the tunnel and pumping system, once completed in 2013, are expected to increase the flow of water into the Gowanus by 40 percent, and reduce combined sewer outflows into the canal by about 34 percent. The measures are mandated by a consent decree from the federal Environmental Protection Administration to bring New York into compliance with the Clean Water Act.