Thames Water has been ordered to give £80,000 to the South East Rivers Trust, a local environmental charity, to make improvements to the polluted river.
It will also pay the Environment Agency’s costs for the investigation of almost £19,000.
In October 2013, an underground sewer pipe in Chislehurst became lodged with tree roots, fat, oil, grease and other debris. The build-up forced sewage above ground, flooding a field and two streams, before entering the River Shuttle.
Officers from the Environment Agency believe the sewage could have been flowing for several days. The effect of the pollution on water quality and river habitats was seen over several miles.
Jamie Lloyd, a land and water officer for the Environment Agency in south-east London, said: “A lack of maintenance by Thames Water over an extended period of time was to blame for this incident.
“Tree roots were allowed to grow into the sewer unchecked, resulting in fat and sewage solids causing a complete blockage. Sewage backed-up and was sent with some force through two manholes, triggering significant pollution. Thames Water compounded the pollution by failing to clear the sewer quickly after the Environment Agency reported the incident to them.”
Thames Water has subsequently relined the sewer and installed monitoring equipment.
The South East Rivers Trust will use the money to install a fish pass on the River Cray at Bexley.