We combined in-depth physicochemical and geochemical characterizations of Toulon Bay seawater (north-western Mediterranean Sea), flow cytometry microbial enumerations and 16S rRNA gene-based high-throughput sequencing of 52 water samples over a high frequency sampling campaign (weekly during 2015, June). The objectives of the study were (i) to study both spatial and temporal patterns in bacterioplankton communities along the contaminated Toulon Bay, (ii) to reveal the main environmental factors driving bacterioplankton communities, more precisely the contribution of trace metals through direct or indirect effects and (iii) to identify the predicted functional response of bacterioplankton communities to chemical contamination in order to assess its influence on the ecosystem functioning.