Tens of thousands of dead fish, mostly pilchards, have been found washed up along Nelson's Maitai River.
A passer-by made the discovery on a busy stretch of waterway on Friday morning.
The Nelson City Council says it could take up to 10 days for the tests to determine the cause of death.
The council says seagulls are eating the dead fish without suffering any ill-effects and there are still living fish in the water.
It says the public health risk should be low, but is advising people not to eat fish caught in the river for a few days.