The River Wensum, which stretches about 44 miles (71km) through Norfolk, is designated as a Site of Special Scientific Interest and Special Area of Conservation.
It is believed to be home to more than 100 plant species and rich invertebrate fauna, and is recognised as one of the most important chalk river habitats in England.
The Environment Agency said its officer “promptly attended the scene” and its investigation concluded: “The most likely cause of the incident was heavy rainfall on Thursday evening flushing contamination from surface water drainage systems into the river.
“This has coincided with a period of low river flows and high temperatures, creating conditions that significantly reduced dissolved oxygen levels in the water.”
It would continue to monitor the river and work with partner organisations, they added.
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