Fishermen examine the damage at the River Quoile
Heavy flooding may have played a part in the deaths of thousands of fish at a popular angling spot near Downpatrick.
The Northern Ireland Environment Agency is investigating the incident on the Quoile River, which was reported at about 0900 BST on Friday.
Local fishermen said one of the best angling spots had become "a graveyard". Perch, pike and eels have been killed.
It is thought that the heavy rain washed vegetation into the water and cut off the oxygen supply to the fish.
An agency spokesman said the incident was most probably down to a lack of oxygen in the water caused by "a natural increase in organic matter".
Norman Henderson from the Environment Agency said: "The experts tell us it was a one in 100 years storm.
Dead fish lying on the banks of the River Quoile
"It washed material into our rivers and lakes that was beyond normal levels.
"As that has broken down so, in turn, it's putting pressure on the rivers."
However, some local people think the river may have been polluted.
Trevor Love, chairman of Down District Angling said: "We're talking tens of thousands of fish killed in this river.
"Of course, these fish will have to be removed somehow. Whose job is this? How are we going to find where the pollution is coming from.
"I think we need to get to the bottom of the situation."
People fear that birds have also been killed after eating the fish.