The foul-smelling black sludge clogging up the river mouth at a Northland beach is not human or animal effluent, but it's still not a good idea to swim in the area, officials say.

The Whangerei District and Northland Regional councils want to quash rumours the effluent-smelling stench and black sludge at Waipu Cove is sewage.

The councils are working together to tackle the problem, which has been the subject of many residents' calls.

NRC environmental officer Jean-Charles Perquin said WDC testing had confirmed it was not sewage, but seaweed and algae which had started to rot in the stagnant stream.

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While such sediment was common "it's been a lot worse this year", Mr Perquin said.

To rule out sewage, WDC staff have checked the sewerage system and taken weekly water samples to test bacteria levels.

"Rotting will have bacteria as it is part of the decomposition process - but it will not hit the 3000 to 4000 e-coli bacteria per hundred million that sewage would show," he said.

Regardless of the cause, it is considered unsafe to swim.

"But Waipu Cove - the beach itself - is clean, and has been clean for the past five weeks [that it's been tested]," said Mr Perquin.

Digging away the banks of the stream to allow the sediment to drain into the ocean could make it unsafe to swim at the cove.

"It's better to keep it contained - it's going to go away anyway."

WDC waste and drainage manager Andrew Carvell said a storm before Christmas could be part of the cause.

"Algae and seaweed got washed in there as well as sand which created areas where water can't escape and it's been decaying - hence the odour," he said.

"There are a lot of people who have complained. Some people who live out here say it's the worst it's ever been."

Waipu Cove surf lifesaving club president Rick Stolwerk said that while the smell had been really bad at the beach the intensity seemed to have subsided.