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Nearly two-thirds of potential water quality issues identified in Otago Regional Council flyover inspections last month were in the Clutha district.
Council staff would begin farm visits this month after the inspections identified about 30 areas across the entire region that could pose risks to water quality, the council said.
A summary of flyover findings released by the council earlier this week said 61% of the identified high-risk areas were in Clutha.
However, the findings could be due to the terrain in the area, the council said.
There were more farms with low-lying areas such as gullies and swales where runoff accumulated in high concentration in South and West Otago.
Planting winter feed in these "critical source areas" and having small buffer zones could increase sediment runoff potential, the council said.
In North Otago, the council identified the risk of surface water ponding on flatter land that lacked drainage.
The summary also listed good farming practices observed in each part of the region.
Council compliance manager Tami Sargeant said that overall, staff were pleased with compliance on farms.
No obvious breaches were identified from the air, she said.
"There are a few high-risk areas where ORC staff will follow up on the ground to make sure good management practices are being followed and to ensure compliance with our rules," Ms Sargeant said.
"These include things like crops being planted in critical source areas — where there is a risk of sediment flowing into waterways — and a few buffer zones near waterways that were narrower than we’d like."
Otago Federated Farmers president Mark Patterson said it was great to see farmers complying with the changes expected by the regional council.
"There’s no doubt it has a bit of a big brother feel to it but it’s the reality with the new world of compliance we’re in. The benefit of it is it identifies areas that can be triaged as at risk," he said.
With the Government watching to see how farmers responded to new compliance rules, farmers had to make sure they were doing the right thing, he said.
"We’ve got to take these things seriously ... there’s no room for error."
Ms Sargeant said it was crucial that winter grazing practices were done with consideration for the environment.
Possible council responses to non-compliance ranged from education and advice to enforcement notices, and prosecution, she said.
Another round of farm inspection flights will take place towards the end of this month.