Graham Simpson, 61, from Ellingham, admitted contaminating the Long Nanny Burn with 3,000 litres of the chemical.
About 60 critically endangered eels also died when his tractor toppled over, the Environment Agency said.
At Berwick Magistrates’ Court, he also admitted discharging kerosene into another part of the river in 2017. He was fined £2,261, with £1,500 costs.
The fertiliser spillage happened in May 2017 and affected the watercourse for six miles (10km) over four days.
Simpson said he believed a faulty rear axle could have caused the tractor to tip over, and he tried to block the drains with soil to absorb the spillage.
The second incident happened in September 2017 when a tank containing heating oil slipped off a forklift truck and polluted the river.
Laura Mollon, from the Environment Agency, said: “Pollution incidents such as this, caused by negligent of reckless breaches of environmental permits, have a serious negative impact on our environment and are something we work hard to prevent.”