Seagrasses are well known ecosystem engineers that can significantly influence local hydrodynamics and the abundance and biodiversity of macrobenthic organisms. This study focuses on the potential role of the seagrass canopy structure in altering the abundance of filter-feeding organisms by modifying the hydrodynamic driven food supply. We quantified the effect of two ecosystem engineers with contrasting canopy properties (i.e. Zostera noltii and Cymodocea nodosa) on the food intake rate of a suspension-feeding bivalve Cerastoderma edule living in these seagrass meadows. Field experiments were carried out in two seagrass beds (Z. noltii and C. nodosa) and bare sediment, located on sandflat characterised by a relatively high hydrodynamic energy from waves and currents. Results demonstrated that the filter-feeding rate was almost twofold increased when C. edule was inhabiting Z. noltii meadows (1.10 ± 0.24 μg Chl g Fresh Weight−1) when compared to cockles living on the bare sediment (0.65 ± 0.14 μg Chl g FW−1). Intermediate values were found within C. nodosa canopy (0.97 ± 0.24 μg Chl g FW−1), but filter feeding rate showed no significant differences with values for Z. noltii meadows. There were no apparent correlations between canopy properties and filter-feeding rates. Our results imply that food refreshment within the seagrass canopies was enough to avoid food depletion. We therefore expect that the ameliorated environmental conditions within vegetated areas (i.e. lower hydrodynamic conditions, higher sediment stability, lower predation pressure…) in combination with sufficient food supply to prevent depletion within both canopies are the main factors underlying our observations.