The Environment Protection Authority (EPA) said the fish were mostly bream, ranging in size from 50 grams to two kilograms.
They were found along about five kilometres of the river and along the bank, near the mouth.
EPA director Wes Ford said there was no sign of pollution in the river.
“We did further inspections to see if there were any obvious signs of pollution – you know, chemical drums or a spill or something – and nothing was found,” he said.
“Probably the most likely natural event occurring is probably a temperature-based event.
“In the upper reaches of the river, we had very cold temperatures a couple of weeks ago.
“You get ice on the surface of the water in the upper reaches – that’s a possible explanation, but it’s really hard to understand and really identify what the nature of the event might be.
“It’s a natural event that occurs in river systems right around the world.”
Mr Ford said the EPA was testing the dead fish and water samples to rule out pollutants in the river.
“All you can do is test the dead fish and see if there’s any evidence of chemical interaction – you know, chemical in the gills.
“You only get a positive outcome in terms of a test if you find something. So the testing results are more likely to be negative and inconclusive and we’re still going to be left wondering.
“We are unlikely to get certainty.”
Mr Ford said while concerning, the event was not extremely significant.
“Any large number of fish, when they get in their thousands, particularly over a relatively small area look like a significant event, but in terms of a context and with the population of fish over there it’s probably still a relatively small number of fish.”