The assessment of ecological quality in the frame of the Water Framework Directive has been performed in Ebre Delta bays (Alfacs and Fangar) using MEDOCC (MEDiterranean OCCidental) index. Results demonstrate the applicability of the index in heavily modified transitional water bodies and its response to pressures (mainly agricultural activities) affecting macroinvertebrate assemblages inhabiting soft bottoms. According to previous studies and the organic matter enrichment and heavy metal gradients inside the bays, three different Transitional Waters (TW) have been distinguished, but only two of them are assigned to Heavily Modified Water Bodies (HMWB). Two different reference conditions have been considered depending on the acting pressures: a Maximum Ecological Potential (MEP) for the areas highly affected by the pressures (i.e., HMWB) and a Reference Condition (RC) for non-modified waters from the southern shelf of Alfacs Bay where the effect of agricultural activity is scarce. A good Ecological Potential/Status (EP/ES) was always achieved in the surveys.