The Church of Scientology Religious Education College in East Grinstead was found to have breached environmental regulations after local people complained of pollution in a tributary of the River Medway.
The stream bed became coated with grey sewage fungus and dead invertebrates were found more than 350 metres downstream after the college replaced its sewage treatment plant in August 2015.
An initial inspection by the Environment Agency in September found the new plant was working properly, but by October 2015 residents in the Saint Hill area raised concerns about pollution.
Inspectors found the new plant was pumping out waste water containing volumes of sewage 10 times over the permitted limit.
They took samples from the treatment plant on 19 occasions - 10 of which failed to meet environmental standards.
The college, based at Saint Hill Manor at East Grinstead, pleaded guilty to one offence of discharging effluent into a watercourse and asked for 10 others to be taken into consideration.
It is a subsidiary of the Church of Scientology, which was founded by science fiction author L Ron Hubbard in the 1950s based on his teachings of psychology, extraterrestrials and rebirth.
Scientology has several high profile devotees, including Tom Cruise and John Travolta.
The college was fined £14,000 and ordered to pay costs of £2,566 at Worthing Magistrates Court.
Dave Willis, area environment manager of the Environment Agency, said: “We are pleased that the court decided to impose a significant financial penalty on the organisation today.
“The incident had a serious and avoidable impact on a local watercourse, caused by failing to ensure that the new treatment plant operated correctly.
“We take these types of incidents very seriously and will do everything within our powers to safeguard the environment and people affected, and that includes bringing those who harm the environment to account for their actions.”
The court heard that the college had been aware of the long-standing problem and was therefore negligent, but has since spent a lot of money to get the treatment plant operating properly.
It also heard that no long-term damage was caused to the waterway.