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Te Whatu Ora has warned that a number of sites within Lyttelton and Akaroa Harbours, including popular spots Akaroa Main Beach, Corsair Bay, Rāpaki Bay, Sandy Bay, Diamond Harbour Beach and Purau Beach Rāpaki Bay, were unsafe to swim in due to the poor water quality.
The health agency said up-to-date information about the safety of swimming spots could be found on the Land Water Aotearoa website.
"Exposure to these could be harmful to swimmers' health which means temporary health warnings may also be issued by Te Whatu Ora. That's why it's really important to check that it is safe to swim at your favourite spot before you jump in.
"After heavy rain, other recreational water sites are also likely to be contaminated from rural and urban run-off.
"As a precaution, avoid swimming in the harbour, rivers, streams, lakes or estuaries for at least 48 hours after heavy or prolonged rainfall, even at sites that usually have good water quality."
People should also avoid eating shellfish from the harbour after heavy rainfall, she said.