The farm was visited as part of a field day, organised by the Otago branch of the Deer Farmers Association, as part of the deer industry conference in Dunedin last week.
Invermay's research farm has a total area of 579ha, comprising 427ha effective. The main deer unit covers 143ha.
The farm had stringent limits it needed to meet under the Otago Regional Council's water quality limits.
The council was invited to the property to "see how bad we were'' when its 6A rules were released, AgResearch scientist Dr Jen Robson said.
With issues over water quality, sediment management and surface water discharge, it was basically non-compliant, she said.
It was decided to use its bad practice as an example, helping other farms improve their properties.
An environmental best-practice focus farm was set up, with a stakeholder group that included deer farmers.
In the past, water quality had been affected by stock access to water.
Stock had affected the clarity and sediment load in streams, while wallows were in close proximity to waterways.
Fencing and drainage solutions were being used to exclude stock from waterways, of which there were about 21km on the property.
About $75,000 had already been spent on fencing 5.2km of waterways and $25,000 on 1600m of drainage.
The problem was that many of the farm's paddocks had waterways and it would be "impossible'' to fence them all.
Other management strategies were being used, including managing deer and sheep together in some paddocks, while deer had been excluded completely from other paddocks.
Wallows had been filled with rocks.
Staff were also looking at managing forage crops which, previously, had been right up to waterways.
The majority of 65ha of forestry blocks were due to be harvested in five to six years.
Many of those blocks lined major waterways and were planted very close to them.
Poor practice from forestry harvest in the past had resulted in sediment loss to waterways.
Future forestry management on the farm would exclude planting in close proximity, and the upcoming harvest should be overseen by farm management to mitigate further loss of sediment.
Silage pit runoff was close to a waterway and was a prohibited activity, which required further investigation.
It might need to be captured and stored to be compliant.
The aim was to have good water quality and, when making farming decisions now, staff needed to think about the impact they were going to have on the environment, Dr Robson said.
It was nice to see koura and "massive'' eels living in streams now, whereas electric fishing in the past had found nothing.
"There's still some issues to work through. At the end of the day, we all want good water quality,'' she said.