After receiving the call from the public, the Northern Ireland Environment Agency (NIEA) sent an inspector to investigate the issue on the river. The report was made on Tuesday evening but, due to poor lighting, the investigation began on Wednesday morning.
It was concluded that the pollutant, which was causing a black discolouration, was coming from a specific tributary upstream of Armagh city.
The NIEA are following a definite line of enquiry and work is ongoing to assess the full extent of the damage.
As part of the investigation statutory samples have been taken and evidence from the river with the view of initiating prosecution proceedings.
The Department of Agriculture, Environment and Rural Affairs and inland fisheries have been notified and will assist as part of a joint investigation.