(Courtesy of the ABC)

A massive algal bloom that has killed thousands of fish at Nhulunbuy, east of Darwin, is expected to resolve itself, Northern Territory Government scientists say.

The Environment Department says the algae is naturally occurring and caused by rain washing nutrients into Port Bradshaw.

Julia Fortune from the Environment Department says the bloom should clear-up during the wet season.

"It's quite common for that to occur in NT waterways, particularly around the commencement of the wet season where a lot of the nutrients and sediment that are stored in the catchment are conveyed to receiving waterways with the commencement of flows in many of these systems that pretty much don't flow during the dry season at all," she said.

The former president of the Nhulunbuy Regional Sports Fishing Club, Peter Cox, says a range of target species were among the 25,000 dead fish.

"I had reports of some medium-sized spanish mackerel up to six to eight kilos," he said.

"Also there were queen fish and trevally amongst them and of course some mangrove jack and a small amount of barramundi, and as we said, bait fish took up a large proportion of the kill."