In the framework of the French Plan National Santé Environnement, the river basin authorities have to implement a comprehensive survey of several organic compounds, including pharmaceuticals in surface waters. Before implementing such a large survey, a list of the priority molecules in terms of their risk to the aquatic environment must be established. Using recent data on the most consumed pharmaceuticals in France and based on the EMEA (2006) model used for human pharmaceutical (ERA), we proposed a list of the priority pharmaceuticals to survey. In this aim, we reviewed and combined physico-chemical properties, fate in wastewater treatment plants (WWTP), pharmacological and ecotoxicological data available from the literature, and implemented a selection methodology. This prioritisation approach allowed us to propose a sound selection of pharmaceuticals and metabolites to survey in WWTP effluent and aquatic ecosystem, which will be discussed. We also evaluated our results for specific pharmaceuticals using data available from literature on removal efficiency of WWTP for biological treatment and on occurrence in effluents and surface waters.