The council was also ordered to pay Enniskillen Magistrates Court analytical costs of £945.21 and court costs of £35.
The council admitted to be struggling to cope with the amount of waste it was receiving at Glassmullagh landfill site near Enniskillen since 1995, however it wasn't until 10 years later that planning permission for a new landfill facility was obtained.
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In 2004 inspectors found water containing very high levels of leachate escaping into a stream which flows into Lough Acrussal.
The landfill site was closed last year when the new Drummee landfill facility opened.
A spokesman for the council said the new facility was at the forefront of waste management and protecting the county's natural beauty was a priority.
Every day up to 8,000 gallons of leachate has to be removed from Glasmullagh by tanker to be treated and disposed of legally.
(GK/JM)
