Thousands of fish have died in a national park near Byron Bay after the local council opened an estuary, leading to a sharp drop in oxygen levels in Tallow Creek.

"It was a massive fish kill, there's no doubt," Dailan Pugh, a local conservationist said, noting the Byron Shire Council shifted at least 12 tonnes of dead fish while others were "swept out to sea".

Thousands of dead fish strewn along Tallow Creek, near Byron Bay, after a mass kill on June 15. Credit:Dailan Pugh

The dead fish included bream, flathead, whiting and eels.

Mr Pugh said he warned council staff last Friday when they began digging a channel through a sand bank separating Tallow Creek from the sea that they risked a repeat of a similar "horrific" fish kill in November 2017.