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Whole Foods is officially coming to the Gowanus Canal!

After years of false-starts, the high-end grocery chain announced on Monday that it will indeed open on its site at Third Avenue and Third Street — five years after touting its plans to build along the contaminated waterway.

Still, Whole Foods has a lot to show for the years of delay that stemmed from cleaning its toxic plot of land and fielding criticism over its proposed 420-space parking lot.

The site is now clean, and the new proposal is even cleaner: the parking plan was reduced to 248 spaces, and Whole Foods reps revealed that 10 percent of the store’s produce will come from a 20,000-square-foot greenhouse on the roof. How’s that, locavores?

“[The new plan] certainly reflects concerns we heard from the community — they made it clear they weren’t happy with the parking garage, and they wanted a greener roof plan,” said Whole Foods spokesman Michael Sinatra. “We delivered.”

The new building — a one-story, 52,000-square-foot megastore similar in size to the chain’s Upper West Side location — will also be 25-percent smaller than the original proposal, which has calmed some jitters about traffic to and from the site midway between Carroll Gardens and Park Slope.

Both neighborhoods have been anxiously awaiting some sort of announcement from the popular store since its inception 2005. But the grocer’s constant indecision over the contaminated site — including reports that it would sell the property and build elsewhere — stalled the process.

Then the Environmental Protection Agency designated the Gowanus Canal a Superfund site, declaring it a national toxic emergency that would need more cleaning. Initially, the state Department of Environmental Conservation had expected the cleanup to be done in conjunction with the Whole Foods construction, but the company pulled out of its store plans even as it made good on the remediation.

But the confusion about whether Whole Foods would build or not is history — though there’s still no timetable for the project. Still, even former naysayers are happy.

“Certainly, we’ll still see an increase in traffic to the area, but I applaud [Whole Foods] for significantly reducing the parking … and the [greenhouse] rooftop and bike access are great,” said Eric McClure of Park Slope Neighbors, who criticized the huge parking garage in the original plan. “They’re definitely taking a positive approach at answering community concerns.”