Microcystins (MCYST) are a group of toxic substances produced by cyanobacteria (‘blue-green-algae’). In case of cyanobacterial blooms microcystin concentrations in surface waters may reach values far above the value proposed as provisional guideline for drinking water by the WHO of 1 µg/L for MCYST-LR. For drinking water production via underground passage it is therefore necessary to ensure removal to a large extent. For this reason experiments with extracellular microcystins were conducted in the laboratory as well as in a natural setting on the UBA’s (German Federal Environmental Agency) experimental field for simulation of underground passage. Laboratory batch experiments showed that adsorption of microcystins can be neglected in sandy material (kd < 1 cm³/g). Batch and column experiments identified biodegradation as the predominant elimination process in these sediments. The degradation rates derived from laboratory column experiments as well as semi-technical scale enclosure experiments varied between 0.2 d–1 and 18 d–1. In the worst case this means a half life of 2.8 days, so that under aerobic conditions contact times of several days should be sufficient to eliminate MCYST to an extent safe for use as drinking water.