Overheating is being blamed for the death of masses of little fish in a lagoon at Otama Beach in the Coromandel.

Analysis of lagoon water samples conducted by the Waikato Regional Council shows low quantities of marine algae is present.

A council spokesperson says none of the species observed are known to be harmful to fish.

'However, water in the lagoon had turned very brown around the time of the fish deaths (last month) and this is thought to have been caused by dissolved organic carbon, such as tannins, entering the lagoon from the surrounding catchment.

'There are many natural sources of dissolved organic carbon such as decaying plant material in a wetland or forest.”

A council scientist noted advice from residents that the lagoon wasn't draining well at the time of the fish deaths and comments the lagoon water was warm.

The intense brown colour of the water would have contributed to the temperature rising by causing the water to absorb more heat than clear seawater.

Since fish can be harmed by high water temperatures, the scientist had concluded that a plausible explanation for the deaths was that the brown freshwater flowing in from the catchment was impounded in the lagoon for a period, and that when it heated up the fish present there were killed.

Given there was no other obvious cause the council has concluded the fish deaths were unlikely to be from anything sinister.

Coromandel-based regional council complaint response officer Wendy Gillett says it's a relief to hear the deaths didn't appear to have been caused by a toxin or algae.

But she says the deaths were concerning and staff would monitor the situation at the lagoon.