The aim of this study was to assess the likely impacts on the ecosystems due to agricultural, human, and industrial activities carried out in an ecologically important area of the Ebro River (Spain). For it, a screening site specific ecological risk assessment was conducted. Considering the presence of high levels of potentially toxic substances, such as metals and chlorinated organic compounds, aqueous and organic extracts were used to assess toxicity in sediments by using the photo-luminescent bacteria Vibrio fischeri (Microtox) as screening response variable. Sediment samples collected during 2005-2006 in the last course of the Ebro River and its Delta have been analyzed. Toxic responses have shown strong relationships to the levels of pollutants in the area. Moreover, various sites presented some toxicity level, probably because of other factors associated with reducing environments into the sediments. Results indicate that Microtox bioassay is an appropriate tool to perform risk assessment studies at screening level.