It is not clear whether sequestration or aging of organic chemicals like polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) limits accumulation in higher levels of aquatic food chains. Therefore, the effect of aging on accumulation was studied in 1-m3 model ecosystems that mimicked fish-dominated, macrophyte-dominated, and fish- and macrophyte-dominated shallow lakes. Also treatments without fish and macrophytes were included. General characteristics, biomasses, total (Soxhlet-extractable), and labile (6-h Tenax-extractable) PCB and PAH concentrations in sediment and biota were monitored over time. Accumulation data for PCB 28, PCB 149, and fluoranthene (native to the sediment taken from the field) were compared to those for spiked analogues PCB 29, PCB 155, and fluoranthene-d10. Labile fractions for spiked compounds were higher than for their native analogues and decreased over time, suggesting sequestration in the sediment. In the majority of cases, 6-h Tenaxextractable concentrations correlated better with concentrations in biota than Soxhlet-extractable concentrations. Ecosystem structure affected food web accumulation, but replicate variability was too high to detect clear treatment effects. Differences in accumulation between spiked compounds and their native analogues indicated an effect of aging for invertebrates, macrophytes, and benthivorous fish. Thus, aging may translate directly into reduced uptake at higher trophic levels.