The main objective of the EU-funded EMCO initiative was to trace and remove emerging water contaminants including drugs, surfactants and textile dyes in polluted European waters. EMCO also aimed to provide comprehensive data on the effluents to compile an emissions list with avoidance strategies. The first step was to identify the expertise available in water treatment together with existing state of the art plants. From this information, a series of new treatments was developed and assessed leading to the selection of appropriate bioassays. From sampling campaigns, it was evident that there was widespread occurrence of emerging contaminants in municipal wastewaters in the west Balkans. Levels of pollutants were significantly higher than in some other European countries and the United States. Using laboratory and pilot-scale plants, the methods proposed by the EMCO project were tested for the level of efficiency in removing the contaminants. In particular reverse osmosis (RO) and nanofiltration (NF) were examined in the provision of safe drinking water. EMCO produced water treatment techniques that were individually tailored to the requirements of target countries and regions. On-site treatment units have reduced the environmental and health risk by improving the surface water quality. A comprehensive series of workshops and publications has distributed the results of the project research to all interested parties.