Mr. Boxshall said much of the waste had been washed down the 150-mile Yarra River that runs through Melbourne into Port Phillip, affecting the city’s bayside beaches the most.

The agency, which takes regular water samples, rates beaches. A “good” rating means that the water is suitable for swimming. “Fair” means that rainfall has affected the water. “Poor” means people should avoid it.

Residents said that the pollution had deterred them from indulging in a favorite summer ritual.

“When the temperature gets above 86 Fahrenheit, Melbournians typically pack the family in the car with food and drink and spend the day at the beach,” said Sam Riley, who lives in the city. “I was going to take my two young boys to the beach myself over the summer, but now I’m concerned about whether the water is clean.”

Mr. Boxshall said any improvement in the beaches’ water quality was uncertain as long as the rain continued. The agency says it usually takes between 24 and 48 hours for the waters to clear after the rain stops.