The Environment Agency was called to the river Beane in Hertfordshire on 11 February after a walker spotted that the river had turned brown and cloudy.
The officers could find no trace of pollution at the time, but returned on 22 February after a period of heavy snowfall to find the river discoloured with a foul odour.
In March the officers traced the pollution over two miles upstream to Allied's production site in Stevenage. Despite staff promises to prevent waste entering the river in future, the pollution continued.
On 17 March, the company told the Agency that the problem stemmed from a misconnection in the site's drainage system. Allied had recently developed a storage area for soya brine that had a drain believed to be connected to the foul sewer. A test revealed it was in fact connected to surface water drains.
The Agency told the company to seal the drain and tanker away waste each day until the misconnection was corrected.
Appearing before Stevenage magistrates on 12 October, Allied pleaded guilty to one charge of causing pollution to enter controlled waters contrary to section 85(1) of the Water Resources Act 1991. It was fined £10,000 with £1,656 costs.