Almost 900 fish have been killed following a leakage of farm effluent at Fardross river in Clogher.
A spokesperson for the Environment and Heritage Service (EHS), said they had received a report of the pollution at the weekend.
She confirmed: "On 26 April EHS received a report of a farm effluent discharge to a tributary of the Blackwater River.
"Officers from EHS and Fisheries Conservancy Board (FCB) investigated the source of the pollution and an initial visual inspection of the area has confirmed a major fish kill, with approximately 870 fish killed, consisting of brown trout and salmon parr. The source was identified as agricultural, and statutory samples have been taken with a view to prosecution."
The kill has sparked calls for higher fines to be imposed on those responsible for this type of pollution.
Green Party MLA Brian Wilson who reported that his group had met with anglers from across Northern Ireland, 'highlighting the problem of pollution in rivers for some time now, yet nothing changes, the situation does not improve'.
"The Environment Minister", he submitted, " must immediately announce an independent Environmental Protection Agency for Northern Ireland, she cannot delay this decision any longer."
At the Green Party's meeting with representatives from angling clubs across Northern Ireland in Stormont on Monday, issues raised included river bailiffs being allowed to take samples from rivers during suspected pollution incidents, offering assistance to the under resourced Environmental and Heritage Service.
There were also calls from the Green Party for severe penalties for those found responsible for river pollution and for the introduction of new by-laws which would allow for the immediate up-grading of septic tanks posing risks to rivers.
Anglers also called for a registrar for chemical usage and the development of proper drainage systems for car washes.
Mr Wilson said: "The longer Arlene Foster delays on announcing an independent Environmental Protection Agency for Northern Ireland, the more polluted our rivers become and the more fish stocks will be destroyed. These pollution incidents cause a great risk to our own drinking water too. The Minister must take action."
