Primary producers are essential organisms for marine ecosystems because they form the basis of food webs, produce half of atmospheric oxygen and are involved in various biogeochemical cycles. At the end of a bloom event, phytoplankton cells are known to produce organic compounds that act as a ‘cement’, allowing the cells to stick together and form large sinking structures called aggregates. These aggregates are microenvironments with chemical properties that are very different from the surrounding water. The main objective of this study was to determine how the temporal variations in cell assemblages over time and the formation of aggregates following a bloom affect the concentrations of molybdenum (Mo) and barium (Ba) in the water column, which are elements typically measured within accretionary hard tissues (e.g., mollusc shells) to track phytoplankton dynamics in the environment. To do so, we performed an environmental monitoring from March to October 2021 at Lanvéoc in the Bay of Brest (France) during which several biological (e.g., variations in phytoplankton assemblages) and chemical (e.g., chemical properties of the water column) parameters were measured once to twice per week. Our results show that spring and summer blooms of Gymnodinium, known to be enriched in Mo, could be one of the reasons explaining the particulate Mo enrichments in the water column. In addition, large phytoplankton aggregates transported a significant amount of Mo to the seafloor and associated suspension feeders. In contrast, the temporal variations in dissolved and particulate Ba concentration were strongly influenced by the formation of diatom blooms. Interestingly, there was a significant shift in Ba from the dissolved to the particulate fraction during the largest diatom bloom in late spring, associated with a significant Ba transport to the seafloor, which may be explained by the adsorption of this element onto diatom frustules. This study therefore highlights the impacts of phytoplankton on the dynamics of these elements in coastal ecosystems.