Severe rain on Boxing Day overwhelmed the city's wastewater systems, and the emergency sewer valve had to be released.
Surf Life Saving said this resulted in contamination in the Taruheru and Turanganui rivers, which flow into Gisborne's beaches.
SafeSwim have also issued a warning not to swim at Waikanae Beach, Wainui Beach, Tolaga Bay and Ocean Beach due to dangerous conditions, including large breaking waves, strong currents and strong winds.
Surf Live Saving eastern region assistant life saving manager Nick Wagstaff is urging people to stay out of the water to avoid the risk of illness.
"We're just advising the public to follow the Gisborne District Council's advice around not swimming in the affected waterways.
"Just coming into contact with contaminated water is too big a risk."
Wagstaff said all patrolled beaches in the area are showing a red water quality alert.
"So we've still got a lifeguard in presence on Midway [Beach], Waikanae [Beach], Wainui [Beach] and Tolaga Bay.
"Our lifeguards will be out on the beaches, roaming, keeping an eye on any public that do go swimming.
On Facebook, Surf Live Saving said the Gisborne District Council was monitoring the situation and will provide updates as conditions change.
The Rhythm and Vines music festival in Gisborne begins on Sunday, with up to 30,000 people are expected to attend over the next three days.
