Abstract Between May 1986 and January 1989, samples were taken on three occasions from the heavily polluted Scheldt estuary, in order to determine the pathways and fate of organic micropollutants. One group parameter (cholinesterase inhibition activity, CHOL) and 30 individual compounds (including chlorobenzenes, chloronitrobenzenes, volatile halocarbons and pesticides) were detected on at least one occasion. Another 10 organic pollutants were identified and quantified by GC/MS analysis. Many other, as yet unidentified, compounds were also present. The River Scheldt appeared to be the major source for most pollutants, although additional emissions along the estuary were also detected. Most pollutants were removed from the water during estuarine mixing (non-conservative behaviour), probably due to various processes, such as volatilization, degradation and photolysis. The fractional loss for most volatile halocarbons was ∼ 75%, but in some cases 100% (e.g., trichloromethane). The fractional loss for CHOL was seasonally dependent: 5–10% in winter, and 35–40% in summer months. For most compounds, reasonable agreement was found when observed sediment-water partition coefficients ( K oc) were compared with predicted values. Pronounced deviations were observed, however, indicating non-equilibrium conditions, probably because of slow sorption kinetics. The concentrations measured in the inflowing freshwater were compared with recently published ecotoxicological freshwater quality objectives. The results show that some organic pollutants (e.g., hexachlorobenzene, CHOL, lindane, 1,1,1-trichloroethane) exceeded the published ecotoxicological risk values in all samples, suggesting that these pollutants may have an impact on the ecosystem of the Scheldt estuary.