The research was carried out in the drained lowland bogs of the Lower San Valley. Special attention was paid to the role of peatbogs in reducing migration of the surplus biogenic and toxic elements. Land drainage carried out in a routine way together with synergistic drainage exploitation of deep waters results in progressing degradation of peat soils. Their capability of accumulating nitrogen, calcium and phosphorus, basic biogenic elements influencing eutrophication of the waters is declining. Mineralizing organic matter becomes a secondary source of pollution, releasing huge amounts of biogenes and toxic heavy metals stored on the surface; this process can be seen well in the profile of degraded fragments of the objects under research. Hydrophobic muck horizons also lose their ability to neutralise extreme conditions of droughts and floods. The remaining peat soils of the San Valley require protection, and even renaturization.