The Environment Agency visited the company in April this year after discovering fat deposits in the river.
The fat had collected on booms put across the river to contain pollution from a previous unrelated incident.
At Apetito's premises officers found deposits of fat around two surface water drains. Returning a week later they found that the drains had not been cleaned up and there was evidence of fresh food waste being tipped into the drain. Another drain was full of fat from an overflowing fat trap.
Chippenham magistrates fined Apetito £5,000 with costs of £1,200.