Longbush Rural Kindergarten general manager said it was decided to close the school on Tuesday after staff found mud and sediment on its grounds.
The team contacted Environment Southland and it was decided to close to protect the safety of the 30 children.
Ms McRobbie said the parents had been supportive and the kindergarten was set to open today.
Environment Southland chief executive Rob Phillips said the regional council team was working with the kindergarten and the farm manager to resolve the situation.
A cleanup has been undertaken and an investigation was under way, he said.
"Our staff have been out to the kindergarten and, although there is no evidence of waterway contamination, mud and sediment has washed through the grounds of the facility from an adjoining paddock."
Mr Phillips said an abatement notice was issued to ensure the farmer stops the run-off immediately.
He was still concerned at some of the intensive winter grazing practices in Southland.
Environment Southland's compliance team was carrying out aerial monitoring and on-the-ground inspections of grazing properties.
He said it was clear some farmers needed to "step up and improve their practices".
Council compliance manager Simon Mapp said council received 10 winter grazing complaints this season.
"We have conducted two aerial inspections for winter grazing so far this winter and are following up with site visits to 76 properties."
