Abstract Disappearance of lakes is one of the most dangerous processes affecting the entire natural environment, including soil. This phenomenon is considered natural, resulting from climate change, however in recent decades, a significant acceleration of this process has been observed due to the direct impact of human activity. In areas directly adjacent to lakes, organic soils usually predominate. Unfortunately, wetlands are increasingly being drained and used for agricultural purposes. Under such circumstances, changes in the physical and chemical properties of these soils are often irreversible, causing their degradation. As an effect of increased mineralization, a number of typical modifications occur in soils, such as carbon loss, increased degree of peat decomposition, and changes in soil structure. Long-term dehydration has led to muck formation. Additionally, lowering of lake water uncovers previously flooded areas and increases the intensity of soil-forming processes. However, the presence of the Subaquatic qualifier in the World Reference Base for Soil Resources (WRB) suggests that sediments in shallow water bodies no more than 200 cm deep can also be classified as soils. The progressive disappearance of lakes observed all over the world is therefore a process affecting not only the reduction of water bodies, but also changes in the properties and typology of soils and vegetation cover.