The Azorean archipelago is composed of nine volcanic islands located in the North Atlantic Ocean, in the the biogeographic macaronesia region (that also includes Madeira Canarias and Cape Verde archipelagos), between 36º 45´and 39º 43´ latitude North and 24º 45´and 31º 17´longitude West. The islands have a total surface area of 2,352 km2 and are spread along a 600 km NW-SE strip. In the frame of the Autonomous Region of the Azores political- administrative statue, the strategic coordination and management of water resources is ensured by the Environment and the Sea Secretary, more concretely through its Regional Department of Land Planning and Water Resources (DROTRH). As a consequence, the strategic lines for the optimization of water resources management are materialized by the Regional Water Plan approved in 2003. This instrument aims to enhace, the sustanability of the water resources, and its operationality in a ten year time bond, as well as to accomplish all legal national and european imperatives. The directive 2000/60/EC of the European Parliament and the Council of 22 December, denominated Water Framework Directive (DQA), establishes a framework for the member states in the field of water policy. One of the most innovative aspects is the introduction of the “Ecological Status” concept for any surface water body type expressed as the deviation from reference “undisturbed” conditions. Overall, the Directive aims at achieving good water status for all waters by 2015. In order to achieve the Water Framework objectives of ecological classification on the basis of biological and physico-chemical results, the Azorean governement launched a monitoring study to classify water bodies of São Miguel and Santa Maria island according to different types of pressures/impacts. Based on this exploratory monitoring programme several results were achieved, for groundwater and surface waters. In general groundwater show two main quality problems, related with pH and microbiological contents, due to agricultural practices and the absence of a generalised sanitation system. The interpretation of the biological data was difficult due to the low level of microalgae and macro-invertebrate diversity, as Azores are an isolated mid-ocean zone. Therefore in order to achieve an ecological classification of surface waters benthonic macrofauna was used as guide. The ecological characterization of the surface water - rivers and lakes – show an high pollution level. As well as for the groundwater, the major sources of surface water pollution are the agricultural activities and lack of sanitation system in a large area of the Azores. Nevertheless, lake waters presented in several cases a good ecological status, despite a few lakes classified as eutrophic.The results gathered in the present study using the coupling of chemical and ecological data, represent the preliminary effort of the implementation of the Water Framework Directive and contributes toward a sustainable management of water resources, which in a small archipelago are constrained by scale.