Switzerland is the source of several of Europe's major rivers. This makes it particularly important to prevent pollution.

Much has been done since the middle of the 20th century to improve water quality by building sewage and effluent treatment plants.

The problem of chemical nutrients entering the lakes has partly been dealt with. Phosphate additives to detergents were the main culprit. These were banned from laundry powder in 1985, but are permitted in dishwashing products. However, manure from farm animals is another source. These nutrients promote the growth of algae, whose effect is to reduce the amount of oxygen in the water and kill off many of the plants and animals living there. It is mainly smaller lakes which are affected, but it is also a problem in Lakes Geneva and Zug.

A tougher problem is posed by micropollutants which cannot be broken down in effluent treatment plants. These include such things as pharmaceutical residues. The long term effects are largely unknown.

The controversial dumping of old munition in some of Switzerland's deep lakes between the 1930s and 1960s has given rise to some public concern, but the local authorities are convinced that they present no danger.

Fish stocks in Switzerland have been falling for several years. The accumulation of several factors is to blame: decreased living space, pollutants, infectious diseases and rising water temperatures.

Another alarm was raised in 2000 when a large proportion of whitefish in Lake Thun were found to have abnormalities in their sex organs. The cause remains unclear.