Murfitt was fined £4,000 for storing waste without a waste management licence and £1,000 for failing to remove waste tyres.
Mildenhall Magistrates court, in Suffolk, also awarded a further £2,718 in costs to the Environment Agency which brought the case.
The Murfitt site in Station Road, Lakenheath, stored tyres within 250m of the Little Ouse River and 100m from homes and the RSPB Lakenheath Fen nature reserve.
There were no systems to protect against the risk of fires or contamination of surface water. The Environment Agency said a fire at the site would have had a substantial impact on the environment and local residents.
Environment Officer, John Harrison, who worked on the case said: Operators who intend to deposit or store controlled waste material should always contact the Environment Agency for advice prior to carrying out the activity.
He added: I was disappointed to find that Murfitt Industries, an operator with considerable experience in dealing with waste tyre materials, did not consider or chose to ignore, the potential environmental impacts and legality of depositing and storing this large quantity of shredded tyres on an unlicensed site.
Murfitt Industries told PRW.com that it would not comment on the case.