Only one of the houseboats is connected to the mains sewer
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Moves to stop raw sewage being flushed directly from houseboats into a Sussex river are under way.
Adur District Council has called on Southern Water, the Environment Agency, and West Sussex County Council to help tackle the problem.
Only one boat at Shoreham is connected to the mains sewer, the council said.
Council leader Neil Parkin said: "Having raw sewage in the river in the 21st Century is unacceptable and we must work together to get this sorted."
Contamination tests
According to the council, the problem was identified when it began compiling a "good practice guide" for houseboat residents.
"It was during the preparation of this document that the scale of the situation with raw sewage in the river came to the surface," a statement said.
The houseboats that are not connected to the mains sewer discharge sewage directly into the river with no treatment apart from maceration - a process that breaks up the waste, it added.
Further sampling of the water, which is tested every month, has now been carried out to establish the extent of the contamination, the council said.
It found that on an incoming tide, the level of bacterial micro-organisms was higher.
Mr Parkin said: "We have written to all the agencies concerned and plan to meet up soon to see how we can collectively use our powers and responsibilities to solve this problem."
The good practice guide for houseboats, which is about to be published, includes planning and environmental advice.