Documents obtained by investigative journalists from SourceMaterial show that Stanlow refinery, run by EET Fuels in Ellesmere Port, Cheshire, regularly exceeded permitted levels of chemical releases over the two-year period, leading the Environment Agency (EA) to determine that permit conditions were broken 58 times.
The refinery, which processes 10 million tonnes of crude oil each year and produces around 18% of the UK's road transport fuel, already faces legal trouble. EET Fuels, formerly known as Essar, pleaded guilty this year to 12 charges of breaching environmental law between 2018 and 2020.
The earlier case concerned separate breaches, while the newly uncovered documents describe other incidents in which toxic chemicals and oil were spilled into waterways and groundwater.
EET Fuels said it "takes its environmental responsibilities extremely seriously".
The Environment Agency has confirmed it is investigating the breaches.
Stanlow is one of only four remaining refineries in the UK. EET Fuels bought the site from Shell in 2011 and holds a permit to operate it. The permit allows controlled amounts of oil and chemicals to be discharged into the air and waterways, but requires the company to make efforts to limit pollution to the environment and harm to humans.