Resuspension of microphytobenthic biomass that builds up during low tide has been acknowledged as a major driver of the highly productive food web of intertidal mudflats. Yet, little is known about the contribution to pelagic food web of the resuspension of other microorganisms such as viruses, picoeukaryotes, cyanobacteria, bacteria, nanoflagellates, and ciliates, living in biofilms associated with microphytobenthos and surficial sediment. In the present study, a novel approach that involves simultaneous Lagrangian and Eulerian surveys enabled to disentangle the effects of resuspension and mixing with offshore waters on the dynamics of water column microorganisms during a rising tide in the presence of waves. Temporal changes in the concentration of microorganisms present in the water column were recorded along a 3 km cross-shore transect and at a fixed subtidal location. In both surveys, physical and biological processes were separated by comparing the time-evolution of sedimentary particles and microorganism concentrations. During a rising tide, sediment erosion under wave action occurred over the lower and upper parts of the mudflat, where erodibility was highest. Although erosion was expected to enrich the water column with the most abundant benthic microorganisms, such as diatoms, bacteria and viruses, enrichment was only observed for nanoflagellates 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 viruses due to resuspension. Ciliate enrichment could not be attributed to resuspension as those organisms were absent from the sediment. Wave agitation during the water flow on the mudflat likely dispersed gregarious ciliates 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 also heavily grazed. Finally, the water column became a less heterotrophic structure in the subtidal part of the semi-enclosed bay, where mixing with offshore waters occurs (50% decrease), compared to the intertidal mudflat, when resuspension occurs. The present study suggests that this differential evolution resulted predominantly from dilution with offshore waters less rich in heterotrophic microorganisms. Indeed, any input of microorganisms accompanying physical transfers due to bed erosion or offshore water mixing was immediately buffered, probably to the benefit of grazers.