The meiofauna represent a highly informative faunal group for ecological evaluation in marine ecosystems, but few studies have investigated their spatial distribution patterns in tidal creeks. As an important component of the tidal flat, tidal creeks tend to have unique, contrasting habitats associated with erosion and accretion beds within a short distance of each other. The gradient represented by these habitats is expected to have consequences on the meiofauna and nematode communities. Based on sediment samples from two tidal creeks on a tidal flat covered with very fine-grained sediments, we show that there are distinct relationships between the benthic habitats, meiofauna/nematode communities and the erosion/accretion status of the tidal creek bed. Although there were no differences in sediment grain size between the eroding and accretion sides of the creek, higher sedimentary phaeopigment, total organic carbon and water contents were observed at the accreting side compared to the eroding side. The meiofauna exhibited a significant spatial variability between the two sides. The dominant taxon, nematodes, was more abundant on the accretion side, whilst copepods were more abundant on the erosion side of the creeks. The nematode/copepod ratio was in agreement with the observation that more pollutants and/or organic matter settled down on the accretion side. A total of 53 nematode genera were identified, belonging to 3 orders and 22 families. The prevalence of tolerant nematode genera such as Desmodora, Sabatieria and Viscosia, suggested that nematodes inhabiting highly dynamic environments are well adapted to the physical disturbance. Our results show that geomorphic evolution as implied by erosion/accretion patterns are reflected in the meiofauna and nematode communities and can be assessed using different community characteristics.