Cyanobacterial toxins are substances produced by cyanobacteria that occur in surface waters world wide. The most common group of cyanobacterial toxins is the group of structurally similar microcystins (MCYST). Sand passage as used in slow sand filtration, artificial recharge and bank filtration has shown to be effective in eliminating microcystins in many cases. For secure drinking water production from surface waters infested by microcystins removal has to be ensured in a wide variety of cases met in the field. It was therefore the aim of experiments in technical and semitechnical scale on the UBA’s experimental field in Berlin to test some worst case scenarios for the reliability of microcystin elimination during sand passage. Experiments were conducted with virgin sand (no previous contact to MCYST) and high filtration rates as well as under anaerobic conditions. The results show that the greatest problem for MCYST elimination can be found under anaerobic conditions as degradation is not complete and may lead to harmful residual concentrations.