Environment crews are investigating a river in western P.E.I. after dozens of fish were found dead Thursday night.

Officials do not yet know how many fish have been destroyed in the Trout River after it was hit with a second fish kill in as many years.Tens of thousands of fish in the Trout River were destroyed last year in a fish kill that affected three rivers, and was described as the worst in decades.

A provincial official holds up two fish killed in the Trout River. (Submitted by Roseanne MacFarlane)

This new kill followed a pattern typical to P.E.I., occurring after a heavy rain Wednesday night washed soil into the river.

The province is investigating the sources of the run off.

It couldn't have come at a worse time. The Trout River had been restocked with thousands of fish just last week.

Dale Cameron discovered the fish kill.

"Any river, no matter how good it is, can only stand so much of this," he said.

Clean up crews spent the day cleaning up dead fish every few steps. Workers will measure and catalogue the fish they find to try to find out how much damage has been done.

"I just can't say what extent we are looking at so far," said provincial freshwater biologist Rosanne MacFarlane.

"The water is extremely red [with soil]. There's no way of knowing right now what caused this kill. Water samples are being collected. Fish samples have been collected as well. And those things will be taken to laboratories and analyzed."

Because the water is so murky, said MacFarlane, she has only been able to see dead fish that have washed up on the rocks or are caught in debris.

"Once the water recedes and clears up, that will be when we see the extent," she said.

Provincial officials were first informed of the kill Thursday evening. At this point, MacFarlane is not sure of how wide an area has been affected, but wildlife officials are optimistic.

"The 2011 fish kill seemed to cover a greater distance of stream and we're just not seeing that in this one," said MacFarlane.

While environment officials are trying to determine the cause of the kill, they will also be looking for a new source of fish to restock the river. The Cardigan Fish Hatchery in eastern P.E.I., which has kept fish for this purpose since the 1930s, has shut down its fish enhancement program.

Two farmers were charged in connection with last year's fish kill for not providing enough of a buffer zone between their fields and waterways. One pleaded guilty but the charges were dismissed against the second.