The aim of the present study was to check the usefulness of the benthic biotic indices proposed for application in the European water framework directive (WFD 2000/60/EC) for the ecological quality classification of coastal water bodies, together with some other benthic methodologies used in different countries of the world. The different approaches were applied in two marine ecosystems affected by the same heavy metal contamination source, coastal waters off Portman and the Mar Menor coastal lagoon, both in SE Spain. Two marine biotic indices proposed for application in the Directive (AMBI and BENTIX) were used, together with community descriptors (abundance, Shannon-Wiener diversity, Margalef's species richness, Pielou's evenness and Simpson's Dominance), the relative benthic index (RBI) and the abundance-biomass comparison method (ABC). Water-sediment interface toxicity bioassays using sea urchin embryos and sediment metal analysis served to check the classifications obtained. The classical community descriptors pointed to a progressive variation in benthic communities along the metal contamination gradient of Portman, but, they did not correctly characterize the environmental status of the lagoon stations. Although the RBI was the index that best classified the sites according to their degree of pollution, the selection of indicator species can bias the results. Since the AMBI, the BENTIX and the ABC method are based on the pollution resulting from organic enrichment, their application in the case of purely toxic pollution may not be successful, as was found to be the case in these two mining-polluted ecosystems. Therefore, the development of new indicator lists according to the type of pollutant may serve to improve the results obtained with organic enrichment-based indices when studying other kinds of disturbance. Finally, we found the toxicity tests to be useful tools for the environmental assessment of aquatic ecosystems, and recommend their inclusion in the WFD.