A two-year multidisciplinary programme has been implemented in the northern part of the Bay of Vilaine area (Brittany, Western France) on the presence and effects of chemicals on estuarine continuums (the Vilaine river and two tidal streams). Pesticide contamination was assessed through the analysis by HPLC-MS of water samples collected by an automatic flow-triggered sampler in the Vilaine and point samples for the other sites. Measurements of PAHs, PBDEs, OCPs, alkylphenols and pharmaceuticals were made on water (dissolved phase and particulate matter), sediment and bivalve samples. Phenylurea and chloroacetanilide herbicides and Irgarol 1051 were the most frequently detected contaminants, with individual concentrations ranging from 0.1 to 1.5 µg/L. Values of the corresponding risk quotients frequently exceeded the threshold value of 1. After rain events, elevated herbicide concentrations were also detected in estuarine sites. PAHs, PBDEs, OCPs, alkylphenols, PCBs and pharmaceuticals were only detected at levels corresponding to baseline levels except for summer period in harbour place where high levels of PAHs were recorded for sediments.