The area is just upstream from the footbridge linking Union Street at Tighes Hill and Islington Park. A floating excavator will remove about 100 square metres of sediment up to a metre deep. A stand of mangroves that has sprouted on the sediment will also be removed.

Hunter Water, which manages this reach of the creek, has said the excavation is to improve water flow and reduce the risk of flooding.

"The sediment and mangroves, if left unmanaged, have the potential to slow the water flow in this section of Throsby Creek," a spokesperson for Hunter Water said in a written statement.

"Removing the sediment and small area of juvenile mangroves will help reduce the potential for flooding impacts in the local area by preventing the spread of mangrove islands and further sediment build up."

John Sutton, a long-time Tighes Hill resident and a prime mover of the environmental revival of Throsby Creek, said he was "reasonably happy" with the removal of the mangroves from this section.

"These are rogue mangroves in an area where the water flow is particularly important," he said. "There has been accumulated sediment, and the mangroves have latched onto it."

Yet the mangroves also signify to him Throsby Creek's gradual return to good health after many years of it being neglected and abused. He has watched these mangroves grow over the past decade or so.

"It's amazing we've got to the point where we can even countenance the removal of the mangroves," he said. "In the 1980s, there were no mangroves along there."

In its statement, Hunter Water said it carried out an environmental review as part of the $200,000 project.

"As mangroves are a protected species, we've completed a Review of Environmental Factors (REF) to guide the works, which will be carried out in accordance with a NSW Fisheries permit," Hunter Water said.

But Mr Sutton, who is a community representative on the Throsby Creek Government Agencies Committee overseeing work to improve the waterway, has expressed "slight concern" that plants are being removed before the release of a mangrove management plan.

That document looking at mangroves is part of the government agencies' five-year plan for the improvement of the Throsby Creek catchment.

"I would like to think this will be the last bunch of mangroves to be removed without that management plan," Mr Sutton said.

The Throsby Creek Mangrove Management Plan is due to be released this month.

The chairman of the Throsby Creek Government Agencies Committee is the state Member for Newcastle Tim Crakanthorp.

Mr Crakanthorp said there was "good science" behind the removal of the mangroves and the sediment.

"I love seeing the creek being revitalised and rejuvenated ... but the restraint of being in an urban catchment is there are lives and people's health and safety that have to be weighed up," Mr Crakanthorp said.

Tom Clarke is another long-time resident and campaigner for the creek's health.

Mr Clarke is delighted to have seen the waterway be gradually transformed in the public mind from "a reviled, smelly drain that didn't feature highly in anyone's estimation" into a "functioning estuary creek".

He said this work was "a proper thing to do, it was part of what was agreed to for the management of the creek".

"It's about time, it's probably past time, for some of the sediment to be removed," Mr Clarke said.

"There's an awful lot of accumulated sediment that's mostly covered by water."

The dredging of Throsby Creek to remove accumulated sediment remains a topic of discussion.

Mr Sutton said it had been more than two decades since the creek was dredged, and he believed it was time for that to be done again.

"I reckon there's already a strong case on an amenity and aesthetics basis," he said, adding that argument flowed into having an impact on how much the community cared for the creek.

On its website, Hunter Water has said there have been going investigations of sediment levels in Throsby Creek and its impact on flooding, to determine if dredging is needed. The next investigation is planned for 2022/2023.

The work to remove the sediment is due to get underway on Tuesday and will take four days.

Read more: The revitalisation of Throsby Creek

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