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A new drainage system meant to keep sewage from flowing into the Gowanus Canal is being circumvented — by dog poop!

That’s right, crap may not be flushing in the fetid waterway from pipes below, but stormwater is causing turds planted by man’s best friend to trickle down from the streets above, according to a local environmental watchdog.

“Basically dogs are the problem — and I’m not saying anything anti-dog, but we have to be realistic,” said Eymund Diegel, a member of the Gowanus Community Advisory Group, which keeps an eye on the $1.2 billion federal Superfund cleanup of the filthy waterway.

The Department of Environmental Protection installed new storm sewers in April to prevent sewage from being dumped into the canal during rainstorms, but water samples taken from the canal by the Carroll Street Bridge showed high levels of microscopic poop following three storms last spring, according to Diegel.

The probes contained more than 24,000 colonies of Enterococcus bacteria — a pathogen found in human and animal intestines — per 100 milliliters in late May and mid-June, which compares to other samples taken from Prospect Park Lake where dogs abound, leading Diegel to conclude that the nabe’s pooches are behind the spike.

“It’s essentially being treated as a toilet,” said Diegel. “It flushes away the poo.”

A rep for the Environmental Protection Agency was at a loss for words upon hearing Diegel’s astonishing revelation at a Gowanus Community Advisory Group meeting on Sept. 24.

“That is surprising,” said Christos Tsiamis, the agency’s Gowanus Superfund project manager.

The Gowanusaur has taken weekly probes of the area for about five years and sends them to a lab in Manhattan, where citizen testers log water qualities across the Five Boroughs for New York City Water Trail Association, a non-profit environmental group.

This reporter joined Diegel during a morning sample session on Sept. 26, gritting my teeth and plugging my nose as I ventured down the canal aboard the environmental planner’s canoe.

The Gowanus Canal may have a bad reputation, but paddling down the canal’s placid, oily surface to the Carroll Street Bridge was actually kind of nice. Sadly, taking a sample required me to plunge my hands into its skeevy depths — known to harbor sewage, toxic waste, and even trace amounts of the clap — but, so far, no rash!

Fortunate for me, Brooklyn hadn’t seen any rain in the last few days, making it unlikely that any serious dog poop had found its way into canal recently, and the odor was only pretty bad.

The feds plan to carve out the dirt from the First Street Basin, one block south of the outflows, and turn the inlet into wetlands as part of the cleanup, and Diegel said the city should reroute the poop water there, where plant life would filter out the crap before it trickles into the canal.

“We would have room to put it in the constructed wetlands and filter basins, which we’re doing anyway,” he said.

A spokesman for the feds said the agency would push the city to remedy the situation in order to make sure separated sewers keep the canal clean, but declined to comment on whether they would divert the runoff to the First Street Basin.

“EPA intends to convey this information to the New York City Department of Environmental Protection and ask them to review this matter to ensure that the new infrastructure functions as designed,” said Elias Rodriguez in an emailed statement.

The Department of Environmental Protection’s press office did not respond to a request for comment.

Reach reporter Kevin Duggan at (718) 260–2511 or by e-mail at kdugg an@cn gloca l.com . Follow him on Twitter @kduggan16.