Meiofauna have a strong role in the functioning of coastal ecosystems but how their food sources affect their community structure remains unclear, likely due to the influence of abiotic parameters and the small size of these organisms. The meiofauna and their potential food sources were sampled in several intertidal habitats (i.e., mudflat, seagrass bed, sandflat) of the Marennes-Oléron Bay, France, and the Sylt-Rømø Bight, Germany, to assess the relationships between habitat characteristics and meiofauna community structure. Biomass and quality (carbon/chlorophyll a ratios) of food sources were estimated. Meiofauna community structure based on density and biomass was determined, as well as nematode diversity and feeding types. Meiofauna density and biomass varied highly within habitats and within ecosystems, ranging from 1.7 × 10⁵ to 3.4 × 10⁶ ind. m⁻² and from 0.057 to 1.541 gC m⁻², respectively. Benthic microalgae and sediment organic matter are important drivers in these food webs as the density of two important trophic groups of nematodes, non-selective deposit feeders and epigrowth feeders, varied in accordance with these food sources. No clear relationship was observed between bacterial biomass and selective deposit feeders (i.e., bacterivores) probably due to the high production rate of bacteria. Complementary information about production rates of food source as well as data from trophic markers would provide complimentary information to better understand flows of organic matter in intertidal habitats, particularly for opportunistic species such as non-selective deposit feeders.