The Hastings District Council has placed warning signs at the sites.
On January 1, Waipuka Stream was identified as a disease risk along with Lake Tutira and the Puhokio Stream at Waimarama Beach.
HBDHB health protection officer Cameron Ormsby said the Hawke's Bay Regional Council monitored bacteria levels weekly at popular swimming spots from Mahia to Central Hawke's Bay.
E.coli was not harmful in itself, but was an indicator that faecal matter was present, he said.
"It is a risk-based system and the Ministry for the Environment sets what are generally safe levels."
When bacteria levels water exceed the ministry guidelines there is a greater risk of skin, ear and eye infections and stomach illness.
"There are times when there is going to be a higher risk to health - generally when it rains heavy enough to wash sheep droppings and cow pats into a river or ocean - that causes a spike in E.coli.
"We ask councils to investigate possible sources of pollution - whether it's cow pats, people with septic tanks that are sodden or something like a pipe going into the river."
He said bacteria levels tend to go up and down in waterways over time - in mid January the Waipuka Stream measured low levels of bacteria. Because it was influenced by ocean tides, there was a greater chance of inconsistent bacteria levels at its river mouth.
It had long featured in Hawke's Bay pollution warnings, but the exact cause was not always easy to identify.
The regional council is carrying out follow-up testing.
People concerned about water quality for bathing can phone the HBRC's Safe Swimming Line on 878 1368, or check its website.
