Whole Foods Market Inc., the organic grocer that includes a commitment to “environmental stewardship” in its mission statement, isn’t green enough for some New Yorkers.

More than a year after announcing plans to clean up a contaminated Brooklyn site to build a supermarket, the company is sparring with residents who say the project will add to pollution and attract unwanted development.

Whole Foods wants to build a 68,000-square-foot at Third Avenue and Third Street on the edge of Park Slope, where the median price of a single-family home is $436,000, almost four times the American median.

Because the store is designed to conform to zoning regulations, approval by the local community board isn’t required. The company’s cleanup plans were approved by New York state, and it needs only a city building permit to proceed.

That hasn’t kept residents such as the campaign coordinator of Park Slope Neighbors, Eric McClure, from complaining, even while speaking favorably about having a Whole Foods store in Brooklyn.

“The community is looking forward to welcoming Whole Foods Market to our neighborhood,” he and Marni Horwitz of Green Roof Brooklyn wrote to the chief executive officer, John Mackey, in a January letter.

The letter, posted on the Park Slope Neighbors Web site, goes on to ask that Whole Foods eliminate a third of its 430 planned parking spots and add a “green roof” with plants and grasses to alleviate pollution. More than 1,200 residents have signed a petition supporting these requests, Mr. McClure said.

The store is to be built on a 2.1-acre tract in the Gowanus Canal corridor that at various times has been used for a junkyard, an oilprocessing facility, and a coal yard. Whole Foods has already started cleaning up the soil, which is contaminated with benzene, a carcinogen, as well as toluene, ethylbenzene, and xylene, according to the New York State Department of Environmental Conservation.

Friends and Residents of Greater Gowanus, a community group, said the cleanup is doing more harm than good. Digging is pushing contaminants into the underground water supply in an area that’s a wetland, a member of the steering committee of the group, which detailed its assertions in a letter to the environmental conservation department, Marlene Donnelly, said.

“We’re spending millions of dollars to clean up the site the right way,” Ms. Minardi said. “The majority of people want us there. It’s only a small group of people hung up on several issues.”