Human activity poses a number of threats to water ecosystems. The most significant of these threats is eutrophication. Eutrophication is typically caused by excess nutrients from agriculture, which end up in water ecosystems.

Another example of human activity drastically modifying water ecosystem is hydraulic engineering. Dams have blocked the flow of many rivers and harnessed them into energy production.

The use of motorboats has been restricted in many Finnish lakes, as it disturbs many water-dwelling organisms. Many invasive species, such as manna grass ja waterweed, also threaten the equilibrium of water ecosystems.

Environmental toxins, such as the insecticide DDT, have ruined many water ecosystems. These toxins have driven many species to the brink of extinction. 

Some Finnish lakes have been troubled by acidification. Acidification is primarily caused by acidic toxins that are spread in rainfall. Nowadays, acidification is not as great a threat as it was some decades before, as the worst emissions from industry and traffic have been somewhat reduced.

Shipping, habitation, traffic and industry all affect the quality of seawater near Helsinki.