Fish and Game was tipped off about a man trying to catch a salmon in the Leith below the university and tracked his vehicle to his workplace.
The man had killed and gutted the fish.
"He had no idea what he'd done was an offence," Fish and Game Otago operations manager Ian Hadland said.
The fish was seized and the man was issued with an offence notice indicating Fish and Game would be investigating and could prosecute.
Spawning trout and salmon, which returned to the Leith at this time of the year, were fully protected under the Conservation Act and taking or disturbing them could result in fines of up to $10,000 and a year's imprisonment, Mr Hadland said.
There had been massive fundraising and hatchery efforts to maintain a viable salmon fishery in Otago Harbour and allowing them to spawn naturally in the Leith was an important part of that, he said.
"Those returning salmon could lay up to 3000 eggs each and they will die shortly after spawning. It's a critical part of their life cycle so they rightfully deserve protection. That's recognised in legislation too."
The Otago branch of the New Zealand Salmon Anglers Association recently released 40,000 smolt into the Leith as part of its long-term project to create a Leith population of salmon.
Branch chairman Wayne Olsen said the man was "flogging a resource" that was there for the whole community.
"We all work for hundreds of hours a year to raise the fish so the whole community can enjoy the recreational fishery. Fishing illegally in any form undoes all the good people do."
Mr Hadland said it was unique to have spawning trout and salmon running up an urban stream like the Leith.
Recent wet weather was drawing the fish in from the harbour as higher water levels provided easier passage.
"There is a lot of fish around at the moment. They are big fish in shallow water and particularly visible. They have nowhere to hide but [there are] plenty of prying eyes."
"By all means, go down there and have a look. Just don't try to catch or disturb them or our officers will be having a chat to you and issuing offence notices."
Both organisations were grateful people had reported the incident.
"We appreciate the help we get from members of the public who alert us to alleged poaching incidents - Fish and Game takes such illegal activity very seriously," Mr Hadland said.
