Rotorua District Council is warning people not to swim or fish in waterways that could be contaminated after heavy rain at the weekend.
The council says sewage ran into some drains and streams during the downpour, and people should avoid these waterways as well as rivers and the harbour until Wednesday.
Utilities operations manager Eric Cawte says drinking water is safe, but people should restrict their use of water after storage levels dropped to just 16% of capacity on Sunday night.
Stoplogs at Ohau Channel on the north-eastern side of Lake Rotorua have been removed to allow water levels to recede.
The Rangitaiki River, which flows into the sea near Whakatane, is due to peak on Tuesday though is not thought likely to cause any flooding.