Locals are demanding to know what killed scores of shellfish in an Auckland marine reserve and whether sediment flows could be to blame.

Officials have launched an investigation after dozens of dead shellfish, mostly cockles, were last week found at the Okura River estuary at the northern end of the Long Bay-Okura Marine Reserve.

Staff from the Ministry for Primary Industries have gathered 40 dying shellfish from the estuary and are carrying out tests to determine if they'd been infected by disease.

Auckland Council was meanwhile pulling together data gathered from the area and had collected extra seawater samples from the Okura River estuary.

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The deaths alarmed the Long Bay Okura Great Park Society, which, before the dead shellfish were discovered, had asked an independent marine biologist to investigate whether sediment flows could be hurting marine life.

The society was concerned that sediment run-off coming down the Okura River from development could be having a major impact.

Society spokesperson Peter Townend said his group had been tracking the polluting sedimentation in the reserve for two years and suspected this had caused the worst ever mass mortality of shellfish in the reserve.

"The health of this reserve is crucial for the health of the wider Hauraki Gulf and the long-term effects on marine and bird life are likely to be dire," he said.

"The rate of mortality has been measured at up to 160 dead shellfish per square metre spanning the entire Okura estuary and out into Karepiro Bay."

The Herald asked Auckland Council whether there could be any link between the latest shellfish deaths and local development activity.

However, compliance monitoring team manager Chris Rawlings said the council was satisfied the WeitiBay development was "operating effectively" and complying with its consent.

The same concerns were raised last year, when WeitiBay chief executive Evan Williams told the Herald that his team were working hard to minimise sediment flow and were meeting all standards, with audits being carried out after every rain event.

The development wasn't the only source of sediment in the area, and that which came off the site also included natural run-off.

An MPI spokesperson said, around New Zealand, it wasn't unusual for there to be mass shellfish deaths in one-off events.

"These are often related to an environmental factor such as storm events or extreme weather conditions."

Mass die-offs could usually be put down to multiple factors.

"For example, this could be attributed to the presence of a pathogen in the shellfish," the spokesperson said.

"That alone would not necessarily kill the shellfish, but when the shellfish are then subjected to an environmental stressor, such as extreme weather conditions or pollution, the shellfish may die."

"MPI is testing shellfish from Long Bay-Okura Marine Reserve to rule out an exotic disease and to try to determine factors contributing to these shellfish deaths."