The aim of this study was to contribute to a better understanding of turbid coastal ecosystems, focusing on spatio-temporal changes at the mesoscale in microphytobenthos structures in a macrotidal bay (Bourgneuf, France). This was based on pigment analysis by high-pressure liquid chromatography (HPLC), reinforced by microscopy observations, in relation to sediment characteristics. Microphytobenthos assemblages of this mudflat were 97% dominated by diatoms, confirmed by HPLC analysis, which showed biomarker pigments of this group: chlorophyll c, fucoxanthin, diadinoxanthin and diatoxanthin. The main assemblage is constituted of epipsammic species, like Plagiogrammopsis, Achnanthes and Cocconeis, characterising mixed sediments. However, this could be replaced by epipelic species, like Plagiotropis, Pleurosigma and Staurophora, during summer due to station silting. Microphytobenthic photosynthetic active biomass in the first 2 mm varied spatially and temporally from 12.2 to 186.9 mg chl a m–2. The predominance of a biomass spatial variability reflected spatial changes in sediment grain size and water content. Biomass in the first 2 mm represented from 28 to 68% of the total amount in the first 10 mm. This indicated an accumulation of biomass in illuminated layers and a biomass decrease with depth associated with increasing values of the ratio of phaeopigments a and fucoxanthin to chlorophyll a (phaeo a/chl a and fuco/chl a). Both could exceed 1.00 in deeper layers. Temporal changes in microphytobenthos structure at the mesoscale were mainly linked to hydrodynamism. This is stronger in winter and responsible for allochthonous pigment input (lutein and phaeophytin b) and sediment mixing, as grazing activity by macro-and meiofauna, forming chlorophyll a breakdown products, is responsible for an increase in fuco/chl a and phaeo a/chl a values during spring/summer.