The deluge overloaded a pumping station near Narooma, allowing stormwater and effluent to wash into the Wagonga inlet.
Producer David Maidment, who is a member of the quality shellfish program, says oysters will be in short supply for a while until the river is completely flushed.
He says containment procedures will guarantee consistent quality.
"Sunday there was a sewage overflow from one of the pump stations, it couldn't cope with the deluge," he said.
Source: ABC News Online