This thesis work aimed to assess the impact of contamination and/or environment on three bivalve species: the Pacific oyster, Crassostrea gigas, the blue mussel, Mytilus edulis and the dark false mussel, Mytilopsis leucophaeata, by studying a battery of biomarkers. Under controlled laboratory conditions, the effects of an antidepressant (fluoxetine) and glyphosate-based herbicides (active matter, commercial formulation and adjuvants) were studied on the physiology of juvenile oysters. Overall, only slight effects were recorded at the tested concentrations (environmental and higher) and exposure durations (28 to 56 days). However, trends and significant differences in mortality, biometric parameters and gametogenesis were especially recorded. For glyphosate-based herbicides, results suggested a higher toxicity of adjuvants and commercial formulation by comparison with active matter. In a second approach, two field studies were conducted on 1) C. Gigas and 2) the two mussel species. In these two field surveys, bivalves were studied in shellfish farming areas and in marinas which strongly differed in the degree of contamination (e. G. Metallic pollution). Regarding M. Leucophaeata, an additional freshwater site was chosen to allow a monitoring along a salinity gradient. The main results of these two field studies showed a higher metallic bioaccumulation in marina environments for the three species. Moreover, in these sites, bivalves were in a poorer physiological condition resulting in: higher mortality rate, slower growth, altered energetic reserves and disruption in reproductive cycle. Biochemical and immunological biomarkers revealed less marked inter-site differences. However, the battery of biomarkers used during these studies allowed us to discriminate differences between shellfish areas which were less contrasted from the contamination point of view. This thesis work provided some helpful knowledge for the European legislations such as “Marine Strategy Framework Directive” which aims to achieve a good environmental status of marine waters by 2020.