The decision taken by Cork Circuit Criminal Court to fine the MMF company £10,000 followed one of the most serious pollution incidents ever in the region.
In 1997 the Martin river, a vital tributary of the Lee, was polluted when pig slurry owned by an offshoot company of Macroom Mills, MMF, leached into the river, killing almost 80,000 salmon and young trout.
At the time the South Western Regional Fisheries Board described the incident as appalling and said it would vigorously seek the prosecution of the polluter.
Yesterday a Macroom Mills spokesman said the pollution of the Martin was deeply regretted, but added the company would appeal the Circuit Court's decision.
The spokesman said that companies working within the Macroom Mills group had been instructed to use "best practice procedures" in their everyday operations, but this time there had been difficulties.
The South West Regional Fisheries Board considered at one stage restocking the river, but it was decided not to do this because of the fear that the introduction of new fish would interfere with the genetic stock of fish in the Martin.
Mr Aidan Barry, manager of the board, told the court yesterday restocking would be "biologically undesirable and would mean that future generations as well as this one would bear the cost of this incident. We prefer to let the river recover naturally, which, while slower, will protect the integrity of the stock. It is our mess. We should carry this cost, not future generations."
The assistant manager of the board, Mr Patrick Buck, said yesterday the court's decision was a landmark which signalled clearly that from now on the polluter would have to pay. "Historically, the environment has played second fiddle to big industry. We are all delighted here. Up to now, the highest fine imposed on industry has been as low as £500."