Recent results show that cylindrospermopsin is more frequent and widespread in surface waters than previously assumed. Studies on the fate of CYN in sediments are lacking, but this is important if these resources are used for drinking-water production via sediment passage. Therefore, the aim of our study was to determine a) CYN retention in two sandy sediments as a function of flow rate, CYN concentration, the presence of DOM and the content of fines (1% and 4%, respectively) and b) the influence of sediment preconditioning and DOM composition of the water (aquatic DOM versus DOM released from lysed cells) on CYN degradation. Retention of CYN proved negligible under the investigated conditions. Degradation in virgin sediments showed the highest lag phases (20 days). Preconditioned sediments showed no lag phase. The presence of aquatic DOM yielded highest degradation rates (k1 ¼0.46 and 0.49 day 1) without a lag phase. Readily available organic carbon sources were preferentially metabolized and hence induced a lag phase. Thus, the presence and composition of DOM in the water proved important for both CYN degradation rates in preconditioned sediments and for the lag phase. Cylindrospermopsin degradation took place solely in the sediment and not in the water body.