Food producer Bakkavor was fined £8,000 for discharging dirty effluent into an Old Leake stream at Boston last week.
It was also ordered to pay full Environment Agency costs of £4,632.
Under its environmental permit, the company can only discharge treated trade liquid from a treatment plant once it has been cleaned to a prescribed standard.
Environment Agency sample testing on 13 May 2011 indicated that the stream was likely to have been polluted for more than a few days which had a significant effect on invertebrates in the water. Low oxygen levels were recorded half a kilometre downstream.
Mrs Claire Corfield, prosecuting for the Agency at Boston Magistrates’ Court, said Bakkavor Foods Ltd had failed to carry out adequate checks to make sure the plant was operating properly.
The company informed investigating officers that a biological culture in the treatment plant may have failed shortly before the pollution. It may have been caused by a change in the type of food products being produced.
Bakkavor also stated that before the pollution there was no in-house sampling to ensure the treatment plant was performing within permit limits. Since then the plant had been decommissioned and the company was getting expert advice on why it failed.