In the absence of chemical or physical gradients, random displacement of organisms can result in unpredictable distribution patterns. In spite of a limited locomotive capability, marine nematodes may choose where to settle after re-suspension and may maintain their position in the sediment under calm conditions, leading to small-scale (<1 m) spatial variability. However, in more energetic environments, nematodes become re-suspended with sediments and re-distributed at distances dependent on prevalent hydrodynamic regimes, from metre- to decametre-scale or more. In this study, we tested the hypothesis that micro-habitats (i.e. runnels and sandbars) in a macrotidal sandy beach influence the distribution patterns of free-living marine nematodes by exhibiting contrasting hydrodynamic regimes. Specifically, we predicted patchier distributions in the calmer environment (runnel). We sampled nematodes in each habitat from <1 m to decametre scales. Our results show more heterogeneous spatial distributions in the runnel, presumably owing to a predominance of active displacement under calmer conditions and sediment cohesion by algal films. Biological similarity among runnel replicates was low, whereas replicates from the sandbar exhibited higher similarity, presumably because of homogenization of the sediment and inhabiting fauna by tidal currents. A significant negative correlation between biological similarity and sampling distance was found in the runnel, but not in the sandbar. The most similar samples were the closest in the runnel and the most distant in the sandbar. More patchily distributed taxa were found in the runnel and a larger fraction of homogeneously or randomly distributed taxa in the sandbar. We conclude that different hydrodynamic regimes in contrasting intertidal micro-habitats significantly influenced the nematofaunal distribution, resulting in different spatial patterns next to one another in the same beach. This has significant implications for sampling and monitoring designs and begs the need for detailed studies about the physical and biological processes governing meiobenthic communities.