High ratios of fecal coliforms, deadly proportions of pathogens, and a low concentration of oxygen have left it generally incompatible with macroscopic marine life, although a variety of extremophiles have been observed in the canal.

[17] The area's early settlers named the waterway "Gowanes Creek" after Gouwane, sachem (chief) of the local Lenape tribe called the Canarsee, who farmed on the shores.

On May 26, 1664, several Breuckelen residents, headed by Brouwer, petitioned Director General Peter Stuyvesant and his Council for permission to dredge a canal at their own expense through the land of Frederick Lubbertsen to supply water to run the mill.

Colonel Daniel Richards, a successful local merchant, advocated building a canal to benefit existing inland industries, and draining the surrounding marshes for land reclamation that would raise property values.

United States Army Corps of Engineers (USACE) Major David Bates Douglass was hired to design the canal, which was essentially complete by 1869.

[33] With the canal's wooden and concrete embankments, the strong tides of fresh diurnal doses of oxygenated water from New York Harbor were barred from flowing into the channel.

This culminated in an incident when a city worker dropped a manhole cover, severely damaging the pump system, which was already suffering from the effects of the corrosive salt water.

[62] CGA founder Salvatore "Buddy" Scotto Jr. referred to the canal as "the most polluted waterway in the world", and "the spine of our deterioration", relating it directly to the economic problems of the area.

[1]: 168 [58] In 2002, the US Army Corps of Engineers entered into a cost-sharing agreement with the DEP to collaborate on a $5 million Ecosystem Restoration Feasibility Study of the Gowanus Canal area.

[76] Initially, local residents resisted the EPA's proposed cleanup methods, as they feared that the toxic waste retrieved from the canal would instead be displaced onto nearby public areas.

[78] The restoration was expected to be paid for by the host of entities deemed "responsible parties" for the pollution by the EPA, including Brooklyn Gas and Electric, now part of National Grid[79] and the City of New York.

[89] The pilot dredging uncovered several artifacts such as a crash boat from World War II; industrial wooden bobbins for textiles; and 19th-century wagon wheels.

[97] The EPA Superfund Gowanus report identified two major PRPs: National Grid (which later acquired Brooklyn Union Gas' successor KeySpan) and the New York City government.

The new design employed a 600 horsepower (450 kW) motor, that pumped an average rate of 200,000,000 US gallons (760,000,000 L; 170,000,000 imp gal) a day of aerated water from the Buttermilk Channel in the Upper New York Bay into the head end of the canal.

According to The New York Times, the proposed plans included steps to "reconstruct the motor pit and replace the propeller with three modern vertical turbines; clean, patch and smooth the interior of the tunnel; replace the broken sewer pipe and encase it in concrete to improve water flow; and reduce the amount of sewer overflow into the canal by increasing capacity at a nearby pumping plant".

The sparsely occupied industrial area offered spaces for studios, music venues, bars, gyms and other businesses that benefited from low space-to-cost ratios.

[110] In 1999, Assemblywoman Joan Millman allocated $100,000 to the Gowanus Canal Community Development Corporation (GCCDC) to produce and distribute a bulkhead study and public access document.

The following year, GCCDC received $270,000 from the New York City Department of Parks and Recreation's Green Street program to construct three street-end public open spaces along the Gowanus Canal.

[17] The New York City government, local citizens' groups, developers, the EPA, and the USACE had a wide variety of concerns and differing visions for redevelopment in the area.

[114] In 1998, the site was proposed for the construction of Brooklyn Commons, a $63 million entertainment and retail complex featuring a 22-screen multiplex cinema, a bowling alley, shops, restaurants and a 1,500-space parking lot.

[59] Perceptions of environmental risk related to pollution and possible flooding vied with the appeal of a diverse community accessible to more expensive areas of New York City.

[125] In November 2006, HABITATS, a festival dedicated to "local action as global wisdom", celebrated the Gowanus Canal with environmental conferences, collaborative art, educational programs and interactive walks around the area.

"[15] The surface of the Gowanus Canal's water has frequently been reported to have an iridescent sheen suggestive of oil, polychlorinated biphenyls (PCBs), coal tar, and other industrial wastes.

Rising gas bubbles betray the decomposition of sewage sludge that on a warm, sultry day produces the Gowanus Canal's notable ripe stench.

[33] One reporter in 1999 described the smell as "like sticking your head into a rubber boot filled with used motor oil and rotten eggs,"[140] while another in 1998 said that it was "less a scent than an assault that reaches in to choke the throat.

[24][137][140] The murky depths of the canal conceal the legacy of its industrial past: cement, oil, mercury, lead, multiple volatile organic compounds, PCBs, coal tar, and other contaminants.

[61]: 327  In 1999, just before the flushing tunnel was reactivated, The Environmental Magazine reported that oxygen levels in the Gowanus Canal measured about 1.5 parts per million;[145] this number continued to be quoted fourteen years later.

Within months of the reopening of the flushing tunnel in 1999, John C. Muir of the Brooklyn Center for the Urban Environment observed pink jellyfish, blue crabs, and a variety of fish.

[45]: 202  The Haques started studying methicillin-resistant Staphylococcus aureus from the canal to learn more about what makes bacteria resistant, so that the research might help to develop new antibiotic drugs.

[166] Thomas Wolfe described the "huge symphonic stink" of the canal which was "cunningly compacted of unnumbered separate putrefactions" in his 1940 novel You Can't Go Home Again.