Residents in Canterbury are being advised to avoid contact with waterways following rain because of potential contamination.
Canterbury Regional Council says heavy rainfall may flush sand and silt from stormwater drains into rivers.
Because of earthquake damage, there is also a risk of sewer overflows.
Canterbury Medical Officer of Health Alistair Humphrey says the risk is much greater at the moment as many sewers and drains are still compromised.
Christchurch City Council says bad weather will give it a better picture of the effects of heavy rain on damaged stormwater and sewer systems.