In Malawi, 22% of the countrys surface area is covered by water, rivers and wetlands Malawi has a significant amount of water in its lakes and rivers. Lake Malawi, Africas second largest natural lake, covers 19 % of Malawis total area.  While groundwater quality is generally acceptable throughout the country, many surface water sources are polluted or under pressure from deforestation, unsustainable agriculture, settlements, mining, industry, commerce, tourism and climate change (flooding and droughts).

Soil erosion caused by deforestation increases sediment loads in rivers that alters directions or restricts river flow, causing flooding and water pollution. Agricultural chemicals, such as inorganic chemicals, herbicides and pesticides, increase nutrient levels in lakes and river, causing the proliferation of algal blooms.

Effluents and solid waste from small and large companies are often dumped into water bodies due to insufficient waste disposal mechanisms. For example, the chemical values in Lilongwe and Mudi Rivers, the main water sources supporting Malawis two largest cities, have been measured above safe limits. Large populations in informal urban settlements with low access to sanitation facilities pose a great health risk to the local residents.