A mysterious brown goo keeps bubbling up from the drains of homes and businesses around the toxic Gowanus Canal — in a neighborhood where a giant, upscale housing complex is set to spring up, The Post has learned.

“It’s a very weird goop,” said Kitty Hernandez, owner of the Brooklyn Colony bar on Fourth Avenue near Carroll Street.

“Just yesterday, I had to pull a drain out because there was a foaming goo coming out of it . . . It overwhelmed the whole bar. I think it was sewage. The smell was horrible,” she said.

The gunk has caused flooding and damages to floors and pipes — up to $50,000, in some cases — at homes and businesses in the hood, sources said.

It oozes from sinks and toilets, often during heavy rain, and may be caused by sewer overflow, which has flooded streets in the low-land area for years during storms, residents and city officials said.

Now, the foul flooding has moved from the streets, indoors — and it’s getting worse, frustrated residents said.

During a rainy night on July 2, the goo caused a nasty toilet backup at the local hot spot, the Bell House, during a book reading, a source said.

It also caused flooding that damaged a car at Family Car Service, said manager Lillian Rodriguez.

Angry business owners claim the city has done nothing to flush away the putrid problem — which has been described as smelling “like rotten eggs” “poop” and “barf.”

“It’s bad. We keep complaining to the city and nothing gets done. They keep promising they’re going to fix it and nothing gets done, ” Rodriguez said.

It’s also a nightmare for landlords in the newly hip hood — alongside one of the nation’s most polluted sites — which could prove tricky for a huge rental complex that will rise next to the Gowanus Canal, which the EPA in 2010 designated a Superfund site, one of the most polluted locations in the nation and in need of immediate cleanup.

“It comes out brown and you say, ‘Oh my God.’ My tenants called 311 to find out what’s going on,” said Joseph Internicola, 67, the landlord of a building on Union Street near Bond Street.

He added, “You have a 700-unit apartment building going up. How are they going to handle it? We’re all going to get backups. It’s crazy.”

Construction on Lightstone Group’s, six-story, $200-million-plus rental complex is set to begin this summer.

The project cleared planning hurdles, despite outcry from neighbors who claimed it would overburden the area’s already stressed sewers.

The city is looking into “if there’s some action we can take to improve the situation,” a spokesman for the Department of Environmental Protection said.

“We did have several reports of flooding and sewer backups in that area,” the spokesman said.

“Our engineers are investigating if any other factors besides heavy rain in short duration is causing this . . . to see if there’s some action we can take to improve the situation,” he said.