This thesis aims at contributing to knowledge about the impact of spatial (land use) and temporal (seasonal, low water levels, rainfall) factors on the resource quality at river basin scale. Thus at risk conditions and areas risk could be identified with the exploitation and interpretation of historical and experimental databases on water quality of the Vilaine’s river basin in Brittany. This study focuses mainly on micropollutants, including pesticides and veterinary pharmaceutical products for the agricultural context, but also on human pharmaceutical products considering the growing interest which is carried in the field of health and environmental risk assessment. In addition, this thesis also proposes to contribute to the improvement and adaptation of human pharmaceuticals treatment in drinking water treatment plant according to regulation evolution and to consumer protection.