The aim of this field study was to investigate the role of mussels on near-bed layer characteristics at different hydrodynamic regimes in a micro-tidal system. At Løgstør Broad, the Limfjorden, Denmark, we deployed ‘siphon mimics’ to sample chlorophyll a (chl a), particulate organic carbon (POC) and inorganic nutrients at different distances above the bottom. This was done without disturbing water column gradients and in a manner similar to mussel incurrent flow. Mimics were deployed at 2 sites: a site with a relatively dense mussel bed and a nearby sandy site without mussels. During the 2 wk field campaign, physical conditions in the fjord varied from extremely calm weather with low waves to quite windy with high waves. Results showed that under all conditions, the vertical concentration profiles of chl a were significantly depleted towards the mussel bed due to mussel filtration, whereas the degree of chl a depletion was correlated to wave height. Nutrient profiles consistently showed increasing concentration profiles towards the bed, identifying the mussel bed and the sediment as a source of nutrients with the highest gradients during the period with high waves. In conclusion, the near-bed concentrations of seston and nutrients in this study were temporally variable and closely linked to the physical structure of the water column.