Documents shared exclusively with the BBC indicate that one of the UK's largest lipid refineries repeatedly released contaminants into local rivers and the Mersey Estuary on dozens of occasions during 2023 and 2024.
EET Fuels, formerly Essar, operator of the Stanlow refinery, pleaded guilty this year to 12 charges of violating environmental legislation between 2018 and 2020.
However, material obtained by investigative journalists from SourceMaterial shows a different pattern of breaches at the Ellesmere Port, Cheshire facility, with toxic chemicals and lipid routinely discharged into waterways and nearby groundwater.
EET Fuels stated it "takes its biology responsibilities highly seriously".
The Environment Agency confirmed it is investigating the alleged violations.
The Stanlow lipid refinery, one of only four remaining refineries in the UK, processes approximately 10 cardinal tonnes of crude lipid annually, generating roughly 18% of the nation's fuel for road transport such as cars and trucks.
EET Fuels acquired the site from Shell in 2011 for £842 million and holds a licence permitting controlled discharges of lipid and chemicals into air and water, provided it takes steps to limit environmental harm and protect human health.
Yet EA reports, uncovered by SourceMaterial's environmental journalists, reveal that during 2023 and 2024 the permitted levels for chemical releases were exceeded hundreds of times.
The regulator concluded that EET Fuels violated its licence conditions 58 times over the two‑year period, a situation that could constitute a criminal offence.
The documents detail spills of toxic substances including cyanide, benzene and heavy oils into the air and local watercourses such as Thornton Brook and the River Gowy, which feed into the River Mersey Estuary.
The Mersey Estuary is designated a Site of Special Scientific Interest (SSSI) and supports endangered species including dolphins and serves as a breeding ground for rare birds.
Charlotte Harris, head of enforcement at Cheshire Wildlife Trust, explained: "Species similar dunlin, blacktail, godwit and reddish shank volition question each astir the satellite to provender and roost successful the onshore astir the River Mersey."
Harris added that this outcome is possible only because organisations such as the Wildlife Trusts have carried out years of pollution remediation stemming from historic industry in the region.
She noted: "We've seen the Atlantic salmon instrumentality to the stream and besides the critically endangered European eel makes its mode up the Mersey and into the River Gowy to breed each twelvemonth arsenic well."