Low oxygen levels and hot weather are believed to have killed thousands of fish in Perth's Swan River.

About 5,000 dead fish were discovered between the Middle Swan Bridge and the Ellen Brook in the upper reaches of the river.

Swan River Trust spokesman Mark Cugley says recent rain and hot weather have decreased oxygen levels in the waterway and that particular area is outside the reach of the river's oxygenation plants.

"Sudden rainfall often drags nutrient-rich organic matter into the river and this typically causes oxygen levels to rapidly drop below levels suitable for fish and other aquatic fauna," he said.

"It is something that is of a concern, and although we believe the cause was low oxygen levels in the water column, we are monitoring the water quality and sending off samples of those fish for that to be clarified."

Mr Cugley says most of the fish appear to be juvenile black bream with the remainder being trumpeter.