A commercial fisherman has been fined $15,000 and had his boat confiscated for illegally taking hundreds of protected golden perch from the Darling River.

Shaun Russell Cox, 36, from Pomona near Mildura pleaded guilty to seven charges of illegal fishing from the river in far west New South Wales, after he was found to be in possession of 146 kilograms of the protected fish species.

He caught the fish near Menindee, where an estimated 3 million native fish died in a string of fish kills over summer.

Cox appeared in the Wentworth Local Court yesterday where he was sentenced.

"A $15,000 fine isn't a great deterrent after losing millions of native fish," Menindee-based water campaigner Graeme McCrabb said.

"It's cost the taxpayer more to investigate and prosecute him than what he was fined."

"It's a slap on the wrist, really."

When Cox was apprehended in March this year, he was found to be in possession of 146 kilograms of the fish, which is the amount he was charged with illegally taking.

But the NSW Department of Primary Industries alleged he took more than 12 tonnes of the fish in total, selling them to Victorian markets for an estimated $200,000.

Their 20-month investigation into Cox also resulted in the seizure of three unlicensed and unregistered firearms and ammunition, for which he was given a 24 month suspended sentence and fined $1,800.

Authorities seized the man's boat, trailer and motor, illegal gill nets, fish and a mobile phone when he was apprehended in March 2019. ( Supplied: NSW Department of Primary Industries )

The court heard Cox had held a commercial fishing license in South Australia in 2012 and 2013, but it had since expired.

Under NSW law, golden perch cannot be fished commercially.

Magistrate Daniel Covington said it gave him "some comfort" that Cox admitted he planned to sell the perch for commercial profit, but remarked he "could have just said he was planning to give them to family and friends".

Magistrate Covington ordered Cox to pay half of the $15,000 fine to the Department of Primary Industries for future research and fish recovery.

He said he believed the fine sent a strong message to Cox and the broader community that illegal fishing would not be tolerated.