Pataua smelled "like death" on Saturday after thousands of dead and dying pipi were blanketed across a shellfish gathering hotspot.
A Whangārei Heads resident broke the news online, saying Pataua's pipi beds were in jeopardy.
"[...]millions of pipi in every size dead the place smells like death [sic]," they wrote.
A video showed a sea of dead pipi strewn across the sandbars between Pataua North and South - popular with seafood gatherers.
Layers of dead molluscs can be seen in the footage each with its shell gaping open.
The Ministry for Primary Industries had been notified about the deaths.
"While such incidents are not uncommon, at this stage the cause is not known," a spokesperson for the ministry said.
Theories shared online included whether the onslaught of heavy rain had made the water too fresh for the pipi to survive.
Another person pondered whether their deaths may be a seasonal occurrence. Others blamed poor water quality and climate change.
The mystery intensified, as according to the local who announced the discovery, cockles, tuatua, mussels, oysters and Karahue Snail were alive amongst the dead pipi.
Live pipi were also found in the water, locals say.
The ministry spokesperson said MPI and the local iwi had teamed up to determine the cause. As part of their investigation samples of the pipi would be collected.
They said in no circumstances should the shellfish be collected or eaten.
More information is expected to be known in the coming days.
The Advocate also contacted the Department of Conservation for further comment.