Heavy rain and flash flooding in early January prompted warnings about inundation of sewerage pumping stations in Merimbula, caused by incorrectly connected stormwater pipes from domestic properties.

It is one of the problems, council's manager, water and sewerage services, Chris Best said, that comes with an ageing sewerage system.

"There are three ways water can get into the sewerage system, through seepage into cracked pipes, localised flooding and the worst one - when run off from roofs and driveways is plumbed into the system," Mr Best said.

He admits that sometimes people can be mistaken when rainwater or run off pipes/gutters have been plumbed into the sewerage system "because it can be hard to tell" but it can also be malicious or just laziness, he said.

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Council has the power to require property owners change their plumbing system if it has been incorrectly connected. Council's compliance team has previously carried out smoke testing of pipes to ascertain where connections go, and have another program planned.

He said it was important to separate out the stormwater and sewage systems to protect our environment.

"When it floods the system works harder; the sewage treatment plant is not working as it normally would.

"You can see a tenfold increase on the normal flow (in the sewer system) in a decent storm and 90 per cent of it is rain," Mr Best said.

"There are designed overflow points such as manholes which can discharge into the environment, grass verges or swales (open grass ditches)."

Pollutants from other sources can also enter waterways during heavy rain, including sewage from household private septic tanks, oil and grease from roads and driveways, sediment from exposed land, and chemicals from gardens.

In a wet weather event when there is an overflow, the sewage is diluted with stormwater, something Mr Best said happens in Sydney multiple times a year, but that didn't mean it was acceptable.

Mr Best said that continued issues with sewer spills in areas of Sydney had resulted in oysters no longer being able to be grown there without purging of biological contaminants before sale (depuration).

"We want the sewer system not to be the primary cause of any lake pollution," he said.

"The worst situation is in dry weather when there is a sewage spill through wet wipes blocking up the system; it backs up and is not diluted," Mr Best explained.

It's a good reason why wet wipes should not be flushed down the toilet, irrespective of what manufacturers may claim for their products.

Mr Best says these are all problems the sewer team are working on as well as designing systems that are larger to better accommodate rain events.