Dobbies, which has a store at Orton Grange near Carlisle, admitted four charges at the city magistrates’ court.
The business was prosecuted by the Environment Agency after a member of the public complained about a foul smell in Sowerby Wood last year.
Jane Morgan, prosecuting, said: "On April 11, an Environment Agency officer responded to a complaint on April 10, that a water course in Sowerby Wood was polluted. The agency had previously received an anonymous complaint on April 2, but on that occasion there was a lack of information."
The officer found that the water course was contaminated with a "white discharge" and "strong sewage odour" which stretched about 1km downstream.
Officers linked it to a pipe pumping secondary-treated sewage into the water from Dobbies. The garden centre had been granted a permit to do this in 2010, ahead of its opening in 2011.
Samples of the polluted water were taken and tested to assess the biochemical oxygen demand: this is measured by the milligrams of oxygen consumed per litre of water. A pristine river would have less than 1mg/l, and the permit granted to Dobbies by the Environment Agency dictates their treated sewage must measure no more than 40mg/l.
Tests on the sample taken on April 11 found it to be 220mg/l, while a further sample taken on April 27 registered 473mg/l – almost 12 times the allowed limit.
Dobbies was charged with four counts of failing to comply with the requirements of the permit. Each charge carried a maximum fine of £50,000.
Two related to keeping the levels below 40mg/l, one was in relation to a failure to ensure the discharge was clear, with no adverse visible effects and the final one related to checks on the discharge.
The permit for the garden centre states that the outlet must be checked weekly. The city magistrates heard that staff were not even aware of this condition, much less carrying it out.
Defence barrister Ruth Stockley told magistrates that while the Environment Agency had spoken with a deputy store manager on April 11 and April 20, it was not until a formal letter was given to Dobbies on April 27 that head office became aware of the issue. Stockley said immediate action was then taken to try to resolve the problem.
Taking into account the early guilty pleas, magistrates fined the company £15,000 for the first breach, £25,000 for the second, £10,000 for the third and £25,000 for failing to carry out weekly checks.
It was also ordered to pay the Environment Agency’s costs of £3,976.08 and a £15 victim surcharge.
Speaking after the case, a Dobbies representative said: "We are taking this matter extremely seriously. Since we became aware that aspects of the sewage treatment plant were not operating as designed, we have been working closely with the Environment Agency and other bodies to rectify the situation. We have admitted liability; however, we are considering an appeal given the unprecedented level of fine."
She added: "We have put rigorous new processes in place and have installed new equipment to minimise the risk of this happening again."