The advice from Bega Valley Shire Council stands for three days following the end of the current rain event.

Pollutants have entered the system from two sewage pump stations that were inundated due to an inflow of stormwater from domestic properties wrongly connected to council's sewerage network.

BVSC manager of water and sewerage services Chris Best said residential stormwater plumbing connected to the sewerage network was an ongoing problem.

"We conduct regular checks to determine which properties have stormwater plumbing connected to the system and we are taking decisive action to reduce the likelihood for further spills," Mr Best said.

Pollutants from other sources 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.

Environmental health coordinator Myf Appleton said the lake will quickly flush the pollutants from the waterway where they will be further diluted when they head out to sea.

"Merimbula Lake is a large waterway permanently open to the ocean. Tidal processes and an increase of water entering the lake will see it returning to normal quickly," Ms Appleton said.

"As a precaution we always advise against entering or fishing in any waterway for three days following a significant rain event."

Council's advice comes a day after it advised people to avoid all water-based activities in Lake Curalo Eden for a week due to a similar influx of pollutants.