Phytoplankton and bacterioplankton are the key components of the organic matter cycle in aquatic ecosystems, and their interactions can impact the transfer of carbon and ecosystem functioning. The aim of this work was to assess the consequences of chemical contamination on the coupling between phytoplankton and bacterioplankton in two contrasting marine coastal ecosystems: lagoon waters and offshore waters. Bacterial carbon demand was sustained by primary carbon production in the offshore situation, suggesting a tight coupling between both compartments. In contrast, in lagoon waters, due to a higher nutrient and organic matter availability, bacteria could rely on allochthonous carbon sources to sustain their carbon requirements, decreasing so the coupling between both compartments. Exposure to chemical contaminants, pesticides and metal trace elements, resulted in a significant inhibition of the metabolic activities (primary production and bacterial carbon demand) involved in the carbon cycle, especially in offshore waters during spring and fall, inducing a significant decrease of the coupling between primary producers and heterotrophs. This coupling loss was even more evident upon sediment resuspension for both ecosystems due to the important release of nutrients and organic matter. Resulting enrichment alleviated the toxic effects of contaminants as indicated by the stimulation of phytoplankton biomass and carbon production, and modified the composition of the phytoplankton community, impacting so the interactions between phytoplankton and bacterioplankton.