Nearly half the shellfish at a monitoring site in one of Auckland's treasured estuaries died over a three-year period, according to a report that has found sediment increasingly choking the marine environment.

If uncontrolled, sediment - including mud and silt - can be washed into the city's waterways and surrounding harbours, devastating marine ecosystems.

The State of the Gulf 2020 report highlighted sediment as one of the Hauraki Gulf's biggest issues, impacting everything from snapper stocks to shellfish beds, and increasing mud at inner-city beaches.

Historically the amount entering waterways increased dramatically after settlers cleared the land of native forest for farming but currently it is linked to urban intensification and building developments in particular.

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Auckland Council has taken efforts to address the issues in the past few years but there are fears that could be undone by the recent emergency budget proposal, which will see half a billion dollars in spending slashed.

An Auckland Council report, which looked at data from October 2015 to April 2018, found nearly all monitored estuaries were "at risk" from an increasing sediment trend.

The worst was at Okura estuary, which runs into the Long Bay-Okura Marine Reserve, where sedimentation had been increasing steadily since 2009, followed by Tūranga and Waikopua. Whangateau had the least number of changes.

At Okura there was a nearly 50 per cent decrease in cockle density at one monitoring site over the recent three-year monitoring period.

Auckland Council Environment and Climate Change Committee chairman Richard Hills said they were "very aware" of concerns around sedimentation and, in November 2018, the council stepped up its monitoring of controls at smaller building sites.

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Previously, council monitoring found about 90 per cent of smaller sites lacked proper erosion control.

Since increasing compliance monitoring, this had dropped to just over 50 per cent.

Even though the sites were small individually, with about 13,500 across the region covering about 600 hectares, they collectively had a large impact.

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Hills said the council was also taking a harder line towards larger developments in sensitive environments than it had in the past, including fighting Todd Property's high-density development of 1000 homes at Okura.

The Government's National Policy Statement on Freshwater had also added impetus to addressing sediment issues.

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While the report showed an increase in sediment levels, it was difficult to pinpoint exactly where it was coming from, Hills said.

"Some is natural but we are doing everything we can to reduce runoff wherever we can, which is why it is important we continue our compliance monitoring programme.

"We are also seeing greater awareness across the board about what goes down the drain ends up in our streams and the sea, and more people are contacting us if they see any issues."

Hills was hopeful the next report, which would factor in the increased monitoring work, would show at least a halt to the increase.

"A few years ago people were really upset with what they were seeing - and often that was some of the older consented work. Now with a council team investigating it seems to be improving."

Long Bay Okura Great Park Society convenor Bruce Usher said the report confirmed what they were seeing on the ground, and they were particularly worried the council's proposed budget cuts could see the small gains halted.

"Our main concern is there is still sediment flowing into the marine reserve. There are council programmes to address it but that proposed budget is going to make it harder."

University of Auckland professor Simon Thrush, who heads the Institute of Marine Science, said problems with sediment started when the forested landscape was cleared for farming, exposing the bare soil to rainfall.

Now urbanisation was the major driver.

"There have been a lot of strategies to address it, including dams near building sites or sumps on drains but clearly more needs to be done. We need a mountains-to-sea approach and everyone can play their part.

"Once sediment enters a waterway, it is very difficult to remove.

"A small quantity will make it turbid, from a nice blue to brown or yellow. Associated with that are effects on shellfish species, filter feeders, which can't then feed properly and are stressed and so don't reproduce.

"Making the water turbid also decreases the amount of light getting to the estuary floor, meaning the microscopic plants that are a primary food source for many species don't grow."

As it makes its way further into the marine environment it can also smother other species and plants, reducing the fish-breeding habitat.

"It really affects a whole range of systems."