The Gowanus Canal, which flowed into businesses on its banks during superstorm Sandy. Photo: Neil Alejandro Photo: Neil Alejandro

In the days after superstorm Sandy flooded the building that housed their film production company alongside Brooklyn’s Gowanus Canal, Kevin Howard and Steven Holtzman had plenty to contend with: Their business, Canal Creatures, lost thousands of dollars of equipment and supplies they had been accumulating for years.

But as much as anything, they worried about the brown goo that coated the floor of the downstairs offices. Like many residents and business owners, they admit that they’d underestimated what they would have to contend with when Sandy hit.

“I didn’t expect toxic sludge to be all over my life,” Holtzman said.

And it was not just the building, but the whole neighborhood that was coated with debris and sludge from the floodwater. Howard and Holtzman watched with alarm as scavengers picked up recyclables left from the deluge and a grocery sold supplies that had been stocked in its flooded storefront.

The water that poured in as Sandy struck flowed from what the U.S. Environmental Protection Agency has deemed “one of the nation’s most extensively contaminated water bodies” and a designated Superfund site since 2010.

Over the weekend, the EPA released findings of samplings from two buildings adjoining the canal as well as from the canal itself. The testing concluded that “chemicals that were tested were below levels of concern or not detected.” What the canal did harbor were high levels of bacteria, likely a byproduct of sewage that ended up in the canal. A separate analysis has found levels 2,400 times higher than the EPA standard for recreational use.

The results offer relief to businesses and residents along the canal whose buildings were inundated with its murky waters and had spent two weeks without guidance on how to safely respond.

For decades, the Gowanus Canal was surrounded by industry — gas and chemical plants, oil refineries, paint factories, cement makers, tanneries — that released all manner of pollutants into its waters. Though a tunnel that brings in freshwater has helped flush out some of the pollution in recent years, the sediment at the bottom of the canal still holds remnants of the past.

Lead, cadmium, arsenic, zinc and mercury are among the heavy metals known to lurk in the canal’s mud, all of them harmful to the health of humans regularly exposed to them. The canal also harbors polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs), both known carcinogens.

Over the past two years, the EPA has been collecting data to help further understand the extent of the contamination there — sampling sediment and fish tissue, evaluating sewer systems and pipes. An investigation concluded that “chemical contamination in the Gowanus Canal sediments presents unacceptable ecological and human health risks.”

The agency is scheduled to select a method for dealing with the pollution by the end of this year.

Jaclyn Jablkowski, communications manager for Build it Green! NYC, an outlet for recycled and surplus building materials, said the nonprofit has been turning to online city websites like the Department of Health and Mental Hygiene to help guide its efforts to sanitize its facility and remaining merchandise.

The staff has been outfitting the groups of volunteers that have showed up to help with gloves and masks, and using bleach to clean up — not a substance this environmentally-minded organization usually keeps lying around.

Build it Green! and its neighbors in an industrial complex along the canal on 9th Street were hit hard by the flooding, which spread between the businesses after knocking down the drywall separating them. Ever since expanding business to the Gowanus location last fall from its first outlet in Astoria, the group has had to deal with occasional flooding from the canal at times of heavy rains; it installed steel barriers to help keep water out. But the blow from Sandy was devastating, Jablowski said, destroying about 80 percent of the inventory there.

She’s hoping that, unlike some of its neighbors, who may be out of business completely, the organization will be able to make it through the setback. It has to: The organization is locked into its lease at the site for another six years.

“We’re hopeful that we’ll be able to bounce back,” she said.

Mears said the EPA is assessing all of its Superfund sites in the city to determine whether the storm has unleashed any environmental trouble. So far, she said, there is no cause for alarm.

Newtown Creek, another Superfund site with a history of toxic discharge from factories, also flooded over during the storm, sending water into nearby buildings and the G train tunnel. The staff of Newtown Creek Alliance, a local advocacy group, is similarly worried about potential contamination from the floodwaters, noting oil sheens and muck left over after they receded. Kate Zidar, executive director of the alliance, has called on the EPA to have a greater presence in the area, also noting concerns about how little is known about the contents of the floodwater.

“We are a Superfund site, so we are taking this very seriously,” she said.

The EPA took water samples in the Newtown area on Friday and is expecting to get results back this week.

In 2005, Hurricane Katrina disrupted a number of Superfund sites in the southern United States and revealed shortcomings in the EPA’s methods of remediating the areas.

While the EPA proceeds with its assessment of Gowanus and other Superfund areas in the city, more immediate health risks are known to lurk in the canal’s water. In an area where sewage overflow frequently contaminates the water, the levels have taken an extraordinary leap since the storm.

Andrew Juhl, an associate research professor at Columbia University’s Lamont-Doherty Earth Institute, has been sampling water all around the Hudson River estuary since 2006. He and his colleagues check for enterococcus, a bacterium commonly used to indicate untreated sewage because it would otherwise only be found in the guts of warm-blooded mammals — and their waste. The Gowanus Canal, like many areas around the city, varies widely in its levels of the bacteria from month to month, Juhl said, though it is one of the most consistently polluted. Testing between 2006 and 2010 showed unacceptable levels of the bacteria — by EPA standards — 50 percent of the time.

Tests from the canal the week of the storm showed enterococcus counts of more than 24,000 per 100 milliliters, Juhl said. The EPA’s cut-off for acceptable levels is 104. In other words, the water is “really, really contaminated,” he said.

These levels are not unheard of, but they usually come when other areas of the city are seeing higher concentrations as well, due to factors like heavy rains that can overwhelm sewage systems. Since this doesn’t appear to be the case everywhere else, Juhl speculates that it could be stemming from a broken pipe near the canal. Tests from a couple of weeks before the storm hit showed much lower enterococcus levels. He and staff from the Riverkeeper advocacy group planned to go back to the area to investigate further.

Juhl notes that sewage contamination and industrial contamination bring different concerns. Sewage is dangerous because of the pathogens that can cause gastrointestinal illnesses or skin rashes — problems that will show up immediately. Even so, he said, it can be difficult to get a sense of how widespread those problems have really been. You can go door-to-door and collect information about individuals who have fallen ill since the storm, but it’s difficult to attribute all the causes of those problems — did someone get sick because they came in contact with floodwater or because they ate food out of a refrigerator that switched off during the storm?

In general, Juhl suggests common-sense precautions, like wearing a mask and gloves when coming into contact with items that have been contaminated with floodwater, and washing hands afterward. It is simple, but it’s sometimes overwhelming in times of crisis.

“Basic hygiene tends to break down when people are stressed,” he said.

Update Nov. 16, 2012:

The EPA’s test results from the Newtown Creek area, released Thursday night, show high levels of bacteria from sewage in floodwaters, but only low or undetectable amounts of industrial pollutants like metals, chemicals and gasoline. The bacteria present in the water will become inactive over time, though the agency notes that people still need to be careful when cleaning up floodwater that contains sewage.

Last week, EPA took two samples in the Newtown area — one from a flooded basement on Eagle Street and one from the creek itself. It had the water tested for bacteria and 139 different chemicals.

As with the Gownaus Canal, the EPA designated Newtown Creek a Superfund site in 2010. Bordering northern Brooklyn and southern Queens, it was once the location of more than 50 industrial sites, including oil refineries, petrochemical plants and factories.