"How and why have we allowed this situation to occur?" Cr Scott asked.
He was commenting on a Catlins water quality and ecological health for rivers report which classified the Taukuku, Maclennan and Tahakopa-upper waterways as excellent, the Catlins sites and Tahakopa-mid site as good and three Owaka sites as fair.
"The percentage of native bush cover upstream reflects the quality of water downstream," water quality scientist Rachel Ozanne said.
The Tautuku River, which had 91% native bush upstream, had excellent water quality and reflected pre-pastoral conditions, while upstream of the Owaka River there was only 20% native bush and water quality was compromised.
Cr Scott wants farmers to be required to permanently fence all streams to help improve the quality of Owaka's water, which showed worrying ecoli bacteria and sedimentation levels.
"Farmers in this particular catchment need to fence streams. It's the only way to stop stock getting into streams."
Chairman Stephen Woodhead said the area was different from other parts of the region as along with farming and forestry, there was a large amount of native bush and a lot of tourism.
"There is an interesting challenge for this area as it is one of the few areas ... that doesn't have a district rural stock water scheme. Combine that with the climate, the soil type, the number of streams - it adds an extra element of challenge."
There was "good stuff" happening in the Catlins by passionate landowners keen to preserve bush and water, he said. Cr Gretchen Robertson said there were only six dairy farms in the region.
The council could not target fencing in the area as it was pursuing an effects-based regime to improve water quality across Otago.
Cr Sam Neill said the report showed water quality in the region was almost all excellent, and asked how far Cr Scott expected farmers to go. Demanding fencing could mean a "draconian" rule.
Cr Trevor Kempton said the council needed to remain consistent in its approach to improving water quality and ensure its ideas were passed on through education programmes.
The report suggested further actions the council could carry out. Chief executive Graeme Martin said those had already been included in the next year's work plans.
They included communicating the findings to iwi and landowners in the Catlins to establish joint initiatives to improve stream health, promote fencing and riparian management, particularly in the Owaka catchment, and investigate the poor water quality in the upper Owaka River.
