The Environment Agency, responsible for protecting rivers and prosecuting water polluters, has been fined £7,500 for polluting the river Exe in Somerset.
Ian Cook, 56, a fly fisherman from Exeter, brought the private prosecution under the Salmon and Freshwater Fisheries Act.
In September 2005, a subcontractor was refurbishing a river monitoring station and inadvertently leaked toxic waste into the main tributary, killing at least 300 fish.
George Prodrick, the owner of the polluted waters, said up to 900 fish could have been killed. He told Exeter Crown Court he saw fish going "belly up" and dying when they swam into the polluted waters.
Mr Cook told the court that Mr Prodrick saw two pipes discharging waste into the river water.
"The Environment Agency sets standards for everyone else. When they fail there is surely greater culpability," Mr Cook said.
The contractor, May Gurney, was fined £27,500 with costs of £1,466. Both the Agency and May Gurney pleaded guilty before magistrates last month to polluting the river.