Priority organic pollutants were investigated in sediments and fish collected along the Ebro river basin (NE Spain) to evaluate their occurrence, transport and bioavailability. Sediments were collected in 18 sites and two species of fish were captured in nine sites according to the availability in each area. The sampling sites covered industrial, urban and agricultural areas. Four methods were used to detect 20 organochlorine compounds (OCs), 8 polycyclic aromatic hydrocarbons, 3 organotin compounds, 2 alkylphenols and 40 polybrominated diphenyl ethers (PBDEs) from purified extracts. The contamination pattern was site specific and no downstream increase in concentration of pollutants was observed but rather a generalized low level diffuse pollution. Target compounds were detected in sediments at 0.01 to 2331 microg/kg dry weight, and only OCs and PBDEs were accumulated in benthopelagic fish. Toxicological assessment was performed according to predicted environmental levels and revealed sites where adverse effects could occur.