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International audience; Resuspension of microphytobenthic biomass that builds up during low tide has been acknowledged as amajor driver of the highly productive food web of intertidal mudflats. Yet, little is known about the contributionto pelagic food web of the resuspension of other microorganisms such as viruses, picoeukaryotes,cyanobacteria, bacteria, nanoflagellates, and ciliates, living in biofilms associated with microphytobenthosand surficial sediment. In the present study, a novel approach that involves simultaneous Lagrangian andEulerian surveys enabled to disentangle the effects of resuspension and mixing with offshore waters on thedynamics of water column microorganisms during a rising tide in the presence of waves. Temporal changesin the concentration of microorganisms present in the water column were recorded along a 3 km cross-shoretransect and at a fixed subtidal location. In both surveys, physical and biological processes were separated bycomparing the time-evolution of sedimentary particles and microorganism concentrations. During a risingtide, sediment erosion under wave action occurred over the lower and upper parts of the mudflat, whereerodibility was highest. Although erosion was expected to enrich the water column with the most abundantbenthic microorganisms, such as diatoms, bacteria and viruses, enrichment was only observed fornanoflagellates and ciliates. Grazing probably overwhelmed erosion transfer for diatoms and bacteria,while adsorption on clayed particles may have masked the expected water column enrichment in free virusesdue to resuspension. Ciliate enrichment could not be attributed to resuspension as those organisms wereabsent from the sediment. Wave agitation during the water flow on the mudflat likely dispersed gregariousciliates over the entire water column. During the rising tide, offshore waters imported more autotrophic,mainly cyanobacteria genus Synechococcus sp. than heterotrophic microorganisms, but this import was alsoheavily grazed. Finally, the water column became a less heterotrophic structure in the subtidal part of thesemi-enclosed bay, where mixing with offshore waters occurs (50% decrease), compared to the intertidalmudflat, when resuspension occurs. The present study suggests that this differential evolution resulted predominantlyfrom dilution with offshore waters less rich in heterotrophic microorganisms. Indeed, any inputof microorganisms accompanying physical transfers due to bed erosion or offshore water mixing was immediatelybuffered, probably to the benefit of grazers.