The Lake Sevan ecosystem started suffering from heavy physical and hydrological interventions. Due to artificial lowering of its water level (up to 20.2m), the morphometric, hydro–physical, hydro-chemical and hydro-biological parameters of the Lake were heavily impacted, causing:

• increase in the water average temperature (in average by 2-3°C);
• significant reduction of the volume of the Lake hypolimnion (bottom layer), pending till almost disappearing from Lake Sevan;
• decrease in water average transparency (parameter characterizing the level of solar radiation penetration/ depth);
• reduction in the dissolved oxygen concentration, especially at the bottom layer;
• reduction in the concentration of phosphorus, increase in concentrations of nitrogen and organic carbon (the balance of the elements has been broken in the basin).

Disruption of the natural balance of the Lake ecosystem caused changes of its hydrobiological characteristics, in particular:

• reduction of layer and biomass of macrophytes (water higher plants serving as a bioindicator of water quality) (macrophytes are an important factor in the Lake water self-purification);
• increase of abundances of phytoplankton, zooplankton and bacterioplankton;
• inactivity of heterotrophic bacteria (heterotrophic bacteria are an important factor in the Lake water self-purification), contributing to the growth of biological organisms causing water pollution intensification, such as massive growth of cyanobacteria (single-celled and colonial organisms contributing to water pollution).
• lessening of fish stocks (also due to overfishing), some species of fish became rare; certain endemic species are lost irreversibly.

Moreover, as a consequence of the Lake water level decline, the length of shoreline has shortened and the Lake surface is reduced, which led to the reduction of the number of endemic species and migratory birds with changes in the basin biodiversity.

Overall changes have shifted the Lake Sevan trophic status from oligotrophic stage (relatively low in nutrients) towards meso- (transitional stage) and eutrophic stages (rich in nutrients). Currently Lake Sevan is in mesotrophic condition.

Since 2002, the Lake level has risen by about 3.5 m as a result of a new management strategy. Unfortunately, the actions to clean and prepare shorelines for raising the water level have not been performed on time. As a result, thousands of acres of forest trees and bushes were flooded, which turned out to be a significant factor negatively affecting the ecosystem of the Lake. A huge amount of biogenic materials, organic carbon, nitrogen, phosphorus, etc., from decomposed forest biomasses integrated into the Lake ecosystem, have become a trigger to empower the eutrophication process.

The Lake Sevan basin is a pool to receive domestic wastewater from nearby territories with a significant negative influence on the water quality. Gavar, Martuni, Vardenis are the only 3 regions in the province to have a system for removing domestic wastewater. Moreover, cleaning systems do not exist along the entire shoreline with touristic and recreation hotspots.

As a matter of fact, another dramatic problem of the Lake Sevan catchment basin is the uncontrolled household garbage and waste, which negatively impacts the Lake ecosystem and water quality. There is no centralized system to remove waste, which turned into a problem of accumulation of garbage in many places and scattered heaps of rubbish. In general, rivers and streams themselves became a means for the population and industrial sector to deliver their garbage into the Lake. The shoreline trash is washed with the river water and precipitation into the Lake. Direct emission of garbage and waste into the Lake water is also frequently happening.

Agriculture and cattle-breeding have a huge share in the negative impact on the ecosystem of the Lake basin through emissions and waste water from fields and farms. Compared to the Soviet period, the use of fertilizers, livestock and large farms in post-soviet Armenia has decreased dramatically and, as a consequence, the pressure of the waste from agricultural lands and livestock on the ecosystem of the Lake has reduced significantly. However, there is still significant pressure on the ecosystem of the Lake from waste of agriculture and livestock, especially in the absence of modern technology.

Mining in the Lake basin in general has a negative impact on the ecosystem (e.g., gold mines of Sotq and chrome mines of Shorzha).

Though the hydro power plants built on about 10 tributaries of the Lake Sevan are small enough, their negative impact on the Lake ecosystem is huge due to changes in water regimes.