Cyanobacterial toxins are toxic substances produced by cyanobacteria or blue-green-algae. The can occur in surface waters wordwide and have to be removed sufficiently when using infested surface waters as drinking water source. Bank filtration has been used since 150 years for drinking water (pre-)treatment and utilizes natural elimination processes like sorption and degardation in the sub-surface. During several research projects the German Federal Environmental Agency (Umweltbundesamt, UBA) carried out field investigations and experiments in different scales in order to assess under which conditions secure elimination of microcystins (the most common group of cyanobacterial toxins) takes place. Filtration of cells on the sediment surface is the most prominent process for eliminating the primarily cell-bound toxins. Middle to coarsly grained sands eliminated more than 99.9 % of intracellular toxins within the first 10 centimeters. Elimination of extracellular microcystin during underground passage is mainly due to biodegradation. Reversible adsorption processes do not reduce the total load but lead to longer contact times for extended biodegradation. Laboratory experiments showed that high clay and silt content is crucial for maximum adsorption. However, redox conditions play an important role for degradation rates: under aerobic conditions half lives of less than one day occured frequently whereas anoxic conditions resulted in lag phases of one day and more as well as in half lives of up to 25 days. Field experiments could show that temperature is crucial for degradation velocity under natural conditions.