Bank filtration (BF) and soil aquifer treatment (SAT) are efficient natural technologies in potable water reuse systems. The removal of many organic micro-pollutants (OMPs) depends on redox-conditions in the subsoil, especially on the availability of molecular oxygen. Due to microbial transformation of particulate and dissolved organic constituents, oxygen can be consumed within short flow distances and induce anoxic and anaerobic conditions. The effect of accumulated particulate organic carbon (POC) on the fate of OMPs in BF and SAT systems is not fully understood. Long-term column experiments with natural sediment cores from the bank of Lake Tegel and from a SAT basin were conducted to investigate the impact of accumulated POC on dissolved organic carbon (DOC) release, on oxygen consumption, on mobilization of iron and manganese, and on the elimination of the organic indicator OMPs. The cores were fed with aerated tap water spiked with OMPs to exclude external POC inputs. Complete oxygen consumption within the first infiltration decimeter in lake sediments caused mobilization of iron, manganese, and DOC. Redox-sensitive OMPs like diclofenac, sulfamethoxazole, formylaminoantipyrine, and gabapentin were eliminated by more than 50% in all sediment cores, but slightly higher residual concentrations were measured in effluents from lake sediments, indicating a negative impact of a high oxygen consumption on OMP removal.