Albania possesses a wealth of aquatic ecosystems, many of enormous natural and biological value, such as the Lakes Ohrid, Prespa and Shkodra, glacial lakes, river valleys, and coastal lagoons. Although many habitats are highly polluted by inorganic and organic wastes, detailed knowledge on the water quality is still lacking. For the first time, an environmental assessment of the water quality is presented and the main polluting sources identified. As a consequence, a systematic control and the establishment of routine monitoring of surface and groundwater is proposed, which elucidates the present environmental state and helps to develop new strategies of waste and wastewater management. It would help allow Albania to reach an international standard in environmental protection, as a part of UNECE Convention, the Mediterranean Action Plan, the MAP/UNEP Medpol Program and the Basel Convention.