Concentrations of several persistent organic pollutants (POPs: PCBs, PBDEs, OCPs) in aquatic species from the Scheldt estuary were related with factors (body size, lipids, trophic position) possibly influencing their bioaccumulation. Stable nitrogen isotope ratios (δ(15)N) were used as a measure for trophic position. A decreasing trend in POP levels toward the sea was observed. For POP concentrations in sediments, this trend could be attributed to a dilution effect from mixing with seawater. However, concentrations in biota more downstream were higher than expected after taking into account the dilution effect, possibly due to differences in bioavailability. Tissue concentrations were correlated with the lipid content in biota, but not with body size. Biomagnification was only significant for some PCB congeners and p,p'-DDE at the most marine sampling location (Terneuzen, L1) and for p,p'-DDD and BDE 100 at the second sampling location (Bath, L2). A significant decreasing relationship was found for γ-HCH concentrations with increasing δ(15)N at Terneuzen. For Antwerpen (L3), no significant relationships were detected. TMFs ranged from 0.64 for γ-HCH up to 1.60 for PCB 194. These results suggest that biomagnification was more important in the marine part of the estuary, although the presence of multiple carbon sources at the freshwater side might have led to an underestimation of the influence of trophic position.