The armed aggression of Armenia against and the occupation of 20 percent of the territories of Azerbaijan have also had serious environmental consequences. Chopping down of forests in the occupied territories, deliberate spreading of fires, destruction of flora and fauna species, pollution of rivers and their tributaries, destruction of fertile soil, illegal exploitation of natural resources by Armenia have inflicted long term and irreversible damage on the environment in Azerbaijan.

Before the occupation, in order to preserve the natural landscape and rare species of plants and animals, various types of reserves (for instance, Basitchay, Lachin, Garagol, Arazboyu, Gubadly, Dashalty) were established in these territories by Azerbaijan.

For instance, the Basitchay State Reserve, established in 1974 in the Basitchay ravine of Zangilan district in the southwest of Azerbaijan, with the overall area of 107 hectares (ha) was well-known for its giant Eastern plane trees. Similarly, established in 1961 in the Lachin district of Azerbaijan, the Lachin State Reserve covered an area of 21 400 ha, where various animal species were protected.

Around 70 388 ha of the specially protected natural areas, more than 261 000 ha of forests, including 13 197 ha of precious forest areas, 215 natural monuments, 5 geologic-paleontological objects, 145 certified eastern planes, aged 120 to 2000 years, with a height of 45 meters, 6 to 8 meters of diameter and other natural monuments existed before the occupation.

More than 460 types of wild trees and shrubs have grown in this area. 70 of them being of the endemic type do not naturally grow anywhere else in the world.

Upon the occupation of the Azerbaijani territories, Armenia have been massively cutting down Eastern planes, walnut, oak and other tree species and selling them to foreign countries.

Furthermore, as a part of its method to utilize natural resources as a weapon, it has been arranging fires to harm Azerbaijani civilians living on the other side of the Line of Contact. Since 2006, as a result of fires set by Armenia, more than 110 000 ha of fertile soil were destroyed, causing serious damage to the environment.

As a result of the above-mentioned activities of Armenia, taxus, corylus colurna, Araz oak, Pterocarya fraxinifolia, Eastern plane, forest grape, ilex, buxus, Eldar pinewood and other trees and shrub species that were protected for many years have become on the edge of vanishing.

Fauna of the occupied territories was also exposed to big losses. As a result of researches conducted with the purpose of animal-recording in the conflict-affected zone, including in Kalbajar, Jabrail, Fizuli, Zangilan, Lachin and Gubadly, it was established that within two years since the beginning of the war, as a result of illegal activities of Armenia, the number of wild animals had been considerably reduced. 

A dense water network in the occupied territories that played a vital role in the formation of water reserves of Azerbaijan was seriously damaged by Armenia.

There were about 120 mineral water wells with high medical treatment potential in the territories subjected to occupation. Among them are, for instance, the Yukhary (Upper) and Ashagy (Lower) Istisu, Baghirsag, Keshdak in the Kalbajar district, Iligsu, Minkand in the Lachin district, Turshsu, Sirlan in Shusha and other mineral waters. 39.6 percent of Azerbaijan’s overall mineral water resources are located in these territories.

Rivers which originate from the Lesser Caucasus mountains, particularly the Tartar, Hakari, Khachinchay, Kondalanchay and other tributaries of the Kura River supplied the low-lying regions with large quantities of water.

Some rivers originating from the territory of Armenia that flow into Kur and Araz Rivers in Azerbaijan are polluted by Armenia with various types of wastes, including chemicals and heavy metals.

For instance, after the liberation of the Azerbaijani territories from occupation, the Ministry of Ecology and Natural Resources of Azerbaijan carried out physical and chemical analysis of the water samples from the transboundary Okhchuchay River located in the liberated Zangilan district near the borderline with Armenia. According to the results of the water analysis, the content of nickel, iron, manganese and the copper-molybdenum compound was higher than the norm. Okhchuchay River contains also perennial heavy metal sedimentations, which causes the extinction of rare fish species. This pollution is a result of the release of heavy metals into the Okhchuchay River by Gajaran Copper-Molybdenum Plant and the Gafan Ore Refinery in Armenia. It ruins the fluvial fauna and is extremely dangerous for the human health. The pollution of Okhchuchay has a direct impact on the quality of water resources of the Araz River - the second largest river in the South Caucasus.

There have been 155 various kinds of mineral resources deposits in the occupied areas, including but not limited to gold, mercury, copper, lead and zinc. The occupied territories are also rich in different types of building materials, including face stone, block stone, different types of construction stones, loam, sang-gravel chromite, lime, marble and agate. These deposits have been largely and illegally exploited by Armenia. Depredatory exploitation of the resources in the occupied territories has severely damaged the environment.

Heavy military equipment, as well as large quantities of exploded shells and landmines caused considerable damage to the soil and flora in the territories subjected to occupation.