Spatiotemporal changes in microphytobenthos species composition were investigated in relation to structural variables—biomass; life‐forms; detritus ratio, pheopigment a (pheo a):chl a; and sediment characteristics—at mesoscale in a shellfish macrotidal ecosystem. To characterize algae assemblages, multivariate analyses were performed (multidimensional scaling [MDS] ordination and clustering), supported by correlations between structural variables. Microphytobenthos, dominated by 97% diatoms belonging to 89 taxa, was constituted by two main assemblages: The first one, composed of common species (occurrence >50%), mainly nanobenthic (size <30 μm) and epipsammic (sand‐fixed cells), was associated with mixed sediments. The major species contributing to this assemblage were Navicula perminuta, Achnanthes hauckiana, Fallacia tenera, A. lanceolata var. elleptica, Amphora spp., Plagiogrammopsis vanheurkii, and Plagiogramma tenuissimum (see Table 2 for taxonomic authors). Species diversity was high (N₁∼ 11), often linked to high biomass values (>70 mg chl a · m⁻²) and low detritus ratio. Conversely, the second assemblage comprised occasional species (occurrence from 10% to 50%), mainly microbenthic (>30 μm) and epipelic (moving cells), occurring during summer at muddy sites. This assemblage, characterized by low diversity, high biomass variability, and high detritus ratio, was dominated by Scolioneis tumida or Plagiotropis vitrea and Navicula spartinetensis. Whereas hydrodynamics globally explained the gradual assemblage changes throughout the entire mudflat and the year, oyster beds and ridge and runnel features appeared to be local spatial structuring factors allowing the establishment of specific assemblages. This study suggests a significant role for epipsammon biomass, until now underestimated, in the functioning of this turbid coastal ecosystem.