An advanced monitoring system is implemented in the refinery. Environmental specialists control pollutant emissions both inside and outside the refinery by means of modern devices.

In 1999–2000 the eco-hydrogeological assessment of aerated soil and ground water within Mažeikiai Refinery area was performed. Oil-contaminated soils have been treated at newly installed oil-contaminated soil regeneration site since the end of 2000.

Since 2000 the tank farm reconstruction has been performed.

In the recent years water and air pollution considerably decreased due to the technical and organization measures implemented. Starting from 1 January 2000 Mažeikių Nafta releases effluents to the Venta river basin and no longer pumping to the Baltic Sea, because quality of treated effluents is several times better as against the established environmental requirements.

The revamp of the last (out of four) sulfur production unit was completed in December 2003. The boilers and burners replaced in all four Claus units during the revamp works started at the beginning of 2002 enabled reduction of pollutant emissions in double.

At the beginning of 2004 the reconstruction of light petroleum product tanks in accordance with EU requirements was completed. Based on the new requirements all light petroleum product tanks have been equipped with pontoons (floating roofs), double seals of pontoons (floating roofs) and painted in white color with sufficient light reflection. The above measures allow minimizing emissions of hydrocarbons evaporated.
A closed-type loading rack was commissioned in January 2004. Since then light petroleum products has been loaded to the rail tank cars at the above rack only. It was installed with a view to minimize evaporation of hydrocarbons during loading process and atmospheric pollution.
In March 2004 the oil sludge treatment unit completely automated was put into operation at its full capacity. This unit is designated for treatment of oil sludge accumulated during sewage water cleaning. After the unit commissioning, oil sludge is no longer accumulated in the lagoons but being processed into oil, water and soil. Separated oil is returned for refining, water is routed to the waste water treatment facilities, and soil is transported to the oil-contaminated soil regeneration site where it gradually turns into decontaminated soil upon treatment by biological preparations.

In 2005 after oil sludge treatment and lagoon emptying, a project of shoreline arrangement (residual oil sludge cleaned and shore treated with biological preparations) was carried out.
In 2005 a construction project of FCC gasoline hydrotreatment unit was initiated in order to meet new environmental requirements for gasoline.
One of the modernization projects implemented in 2005 – butane-butene alkylation – is also associated with the new gasoline requirements and designated for compliance with more stringent requirements for aromatic hydrocarbons. After the project completion the refinery has replaced a part of gasoline components with the other ones - high-octane components of distinctly different structure. Butane fraction is not very preferred as a component for LPG and for domestic gas. A part of unsaturated hydrocarbons - butenes - will be used in this process. [Project benefit is not clear]
One of the projects provides switching of production mode from MTBE (methyl-tret-butyl ether) to ETBE (ethyl-tret-butyl ether ). Performance properties of the above components are similar, however ETBE usage instead of MTBE would allow dealing with transportation and storage issues during winter season since ETBE boiling point is lower and it is less volatile. [benefit is not clear]
Vacuum residue deasphalting unit will serve for the major positive environmental impact. Vacuum residue is bottom-of-the-barrel fraction accumulating the major part of heavy hydrocarbons as well as high-molecular components which are hardly possible to be applied as fuel.

On 16 June 2006 a new oil sludge site (oil-contaminated soil regeneration area) was placed in operation. The soil obtained upon oil sludge treatment with biological preparations is stored at this site.
The oil-contaminated soil regeneration site has been expanded by additional 1,4 ha due to increased treated soil volumes; therefore site capacity reached up to 12000 tons per year.
Based on soil regeneration site project 13 500 m² concrete platform with embankment around it and water collecting to the one side of the area and connection to the sewage network was installed.
Layers of film and geotextile area were applied for the protection of soil under the concrete coatings. Two monitored bore wells for underground water monitoring were made.
Petroleum product truck loading terminal has been upgraded with closed-type loading and vapor recovery system. On 20 December 2006 the State Commission accepted the new petroleum product loading terminal of Mazeikiu Nafta as fit for service and meeting all relevant requirements.
The terminal loading rack contains qualities - precise compliance with environmental requirements is one of the most important ones. While product loading all gasoline and diesel vapors expelled from a truck tank are caught by a separate hose and routed to the vapor recovery unit where hydrocarbons separated are returned back to product tanks at the end of the process.