Environmental scientist Paul Scholes said the regional council was working with landowners above Kaiate Falls to fence and plant the waterways on their properties to improve water quality.
"Most properties are now fenced but it may take time to see the benefits."
Fencing off and planting waterways removed stock access, which stopped faecal matter going to the water while also reducing bank erosion and in some cases, filtered run-off.
Mr Scholes said records of elevated bacterial levels at McLaren Falls after heavy rainfall were less frequent in the past two, relatively dry, summers.
Since 2012 the regional council and landowners had protected 57 kilometres of waterway in the Wairoa catchment, which included McLaren Falls.
"It's a major task to address the many thousands of kilometres of stream length that passes through agricultural and urban areas," he said.
It took time to spur the array of groups needed to make change into action, he added.
"Change often requires co-operation of landowners, iwi, community groups, industry stakeholders and local government agencies."
Tourism Bay of Plenty head of marketing Kath Low said the Bay prided itself in being a destination rich in natural assets.
"Pollution of any kind detracts from that and is something that shames us all."
David Hindmarsh of Ridge Country Retreat, 3km from Kaiate Falls, said it was disappointing he couldn't recommend the falls as a safe swimming spot.
"It's a beautiful place but I can't recommend it to guests."
He had been at the retreat for four and a half years and the falls had been unsafe during that whole time, he said.
"Guests have swum in it, either they don't bother to read the sign or they do and just go anyway. We haven't had any feedback on illness, though."
Mr Hindmarsh said it was a shame not a lot of progress had been made on cleaning the stream up. "We got a man on the moon and we can't solve this problem," he said.
A Ministry of Environment spokeswoman said to support councils to improve freshwater quality the government had put a framework in place that set national standards for fresh water quality.
The regional council was implementing the National Policy Statement for Freshwater.
Each year the Bay of Plenty Regional Council monitored rivers and lakes for faecal contamination from October to March.
Readers react
'Unacceptable' level of poo at popular Bay swim spots
Daniel Lee: Our green image is slowing turning brown ...
Tania Turei: Not taking my boys there any more
Viv Proffitt: How are these stream being polluted, are they running next to farmland? Or through the bush? If through bush, is it possum causing this?
Ngarimu Voss: Is there an acceptable level of poo at swimming spots?
