In 2004, the Austin, Texas-based gourmet grocery chain Whole Foods Market, which by now has five Manhattan stores, said it was going to open a store the next year on a mostly empty lot at the southwest corner of Third Avenue and 3rd Street in Brooklyn. The next year came, and Whole Foods announced a new opening date: early 2007. Early 2007 came; there was no Whole Foods in Gowanus.

In the last quarter, the chain posted a 31% net income loss, and announced it is “revising” — not abandoning — its Brooklyn plans.

That Whole Foods should still be thinking of opening a store on a toxic floodplain (hence the delays) tells us something about the site. Namely, it’s a location too good to be true. The same may be said of much of the oft-maligned part of Brooklyn called Gowanus.

Gowanus is the neighborhood along both banks of the Gowanus Canal, abutting Park Slope to the east and shading into Carroll Gardens to the west. Once, there was a Gowanus Creek, a meandering freshwater stream that flowed from Gowanus Bay (which separates the South Brooklyn neighborhoods of Red Hook and Sunset Park) approximately as far north as the canal extends today, or roughly to Douglass Street in Boerum Hill, a neighborhood once known as North Gowanus.

In the 1850s the creek was straightened out to be made into a navigable canal to serve inland industries. It got its biggest boost in 1869, when Edwin Litchfield dredged it, drained the neighboring marshlands, and built four sizable basins, along which factories and warehouses flourished until after World War II. A number of factories and warehouses, some still making use of the waterway, operate there to this day.

Litchfield owned the land that sloped westward from Brooklyn’s terminal moraine, atop which in 1854-57 he built his spectacular house, later absorbed into Prospect Park and still standing.

On the upper portion of Litchfield’s land rose the late-19th-century neighborhood of Park Slope. The marshy lowlands, Litchfield felt, were unsuitable for fine residences, but perfect for a canal, factories, and warehouses, interspersed with humble homes of factory workers.

As factories were built, the canal became horribly polluted. The water became an oily sludge with a sickly lavender color and an unbearable stench. In 1911 a great pump was constructed at the northern end of the canal so that fresh water could regularly flush out the channel.

The pump broke in the 1960s. All the ordinary delays ran up against the 1970s fiscal crisis, and the pump stayed broken. The canal re-putrefied until 1999, when the pump was fixed — and, we believed, a new day had dawned for Gowanus.

By then, Park Slope and Carroll Gardens were scorchingly hot real estate markets. Visions emerged of splendors that might rise along the waterway’s banks — some invoked Venice, others San Antonio — infilling this once seemingly impenetrable divider between the two neighborhoods.

It’s been slow to happen. Toxic residues left from the halcyon industrial days have proved a greater problem than developers expected. Cleanup costs are sky-high — and perhaps can’t be justified in the recent economic downturn. Some environmental scientists even say that much of Gowanus’s ground is so contaminated it simply cannot be adequately cleaned up, at any cost.

And the old pump should have been replaced, not repaired; its inefficiency hasn’t quite cleaned up the canal as we’d hoped. The city says it will build a new pump, to be ready in 2012. With city projects stalling left and right for want of funds, it’s likely we’ll miss that goal.

Meantime, Gowanus goes its sweet way. The vistas stun, the old bridges crossing the canal are beauties, there are classic factories and warehouses, and artists and arts organizations have flocked to the area.

In 2006, the New York City Landmarks Preservation Commission landmarked the New York and Long Island Coignet Stone Company Building, which stands at the southwest corner of Third Avenue and 3rd Street, on Whole Foods’s property. Designed by William Field & Son and built in 1872-73, it’s the oldest known concrete building in the city.

It served as offices of a large concrete manufacturing complex specializing in the patented Beton Coignet that was invented in France in the 1850s. Now in an advanced state of deterioration, it had artificial brick put on it in the 1960s. The two-story Italianate building looks as though it’s an old mansion incongruously set in an industrial wasteland.

The architecture critic Lewis Mumford took a walk around Gowanus in 1952, and described “grimy factories and warehouses and gas tanks” and “empty lots and industrial rubble” — evoking “a segment of a bombed city.”

In the midst of this emptiness, the Brooklyn Improvement Company, whatever that may be, occupies a classic stucco mansion, standing … in ironic solitude — or should one say hopeful anticipation?

Brooklyn Improvement Company was the name of Litchfield’s concern, which owned the land the concrete company occupied. That company was short-lived, and by 1882 the Brooklyn Improvement Company had made the “stucco mansion” its own offices, which it would inhabit until 1957.

Fifty-six years after Mumford wrote, and we still don’t know if it’s ironic solitude or hopeful anticipation.

fmorrone@nysun.com