Scottish Water earned the biggest fine of £10,000 for polluting Torry Burn, near Cairneyhill in West Fife.
The firm pleaded guilty to contravening its water use licence, contrary to section 40(1)(d) of the Regulations, at Dunfermline sheriff court on 23 January.
A member of the public reported a discharge entering the burn from Cairneyhill sewage pumping station in April 2006. On visiting the site, SEPA officers discovered the river was grey and smelt of sewage and was heavily contaminated with sewage fungus downstream of the pumping station.
The leak had also affected invertebrate communities for up to a kilometre.
Discharges are permitted if the tanks overfill during storms but the flow rate through the works was not high enough to justify the tanks’ use at the time.
The Agency blamed the problem on the plant’s pumping station and estimated that sewage had been discharging into the Exe at up to 400 litres per second for more than a week. In total, more than 84,000 cubic metres were released unnecessarily, posing a risk to shellfish beds further downstream.
Wessex used tankers to remove sewage from the blocked sewer and Bugmore Drain. But the Agency says the river still suffered "significant contamination", which could have been avoided if the company had monitored its overflows better.
Wessex has now fitted a recording device at the overflow.
Appearing before Salisbury magistrates on 9 January, Wessex pleaded guilty to causing sewage to enter controlled waters, contrary to section 85(1) of the 1991 Act.