The paper aims a review of the water quality monitoring and evaluation studies conducted at National R&D Institute for Industrial Ecology over the last ten years, at the level of aquatic ecosystem complexes in the Danube Delta. The paper will include a broad compendium of data including: a data bank of abiotic variables which control the structure and composition of biotic communities; studies of ecological status assessment; methodology development for assessing the bioaccumulation of chemical pollutants (metals) in the biota; ecotoxicological study of surface water and sediment on aquatic organisms (algae, crustaceans, rotifers); studies on the benthic invertebrate species as biological vectors for pathogens; technical / scientific support for 5 national / international project proposals; 19 papers published in international / national journals; 22 papers presented at international / national scientific conferences.