The blaze at Allied's Bradford headquarters destroyed its main warehouse last week, but as it was brought under control chemicals leaked into nearby rivers.
A spokeswoman for the National Rivers Authority in Leeds said: 'There has been a serious amount of damage and destruction to invertebrate life in the River Calder.'
She added that some fish had died, and while the pollution was thinning as it travelled downstream, there was risk of damage to the River Aire and the Humber.
The company estimates the damage at around pounds 6m, and said it has third-party insurance to cover pollution damage.
Allied shares fell from 174p to 166p yesterday. The stockbroker Hoare Govett has taken a particularly bearish stance. Martin Evans, an analyst, said: 'The building will be insured but the fire will cause massive disruption. It hit Allied's main warehouse.'Reuse content