This study was conducted to investigate the spatiotemporal variability in subtidal meiofaunal assemblages off the southern coast of Korea at local and regional scales. Abiotic and biotic samples were collected by site (three sites at least 10 km apart) within region (three coastal regions at least 50 km apart) over 7 years (2015–2021). The density and taxon richness of meiofaunal assemblages differed significantly among sites, but not among regions or years. The meiofaunal assemblage composition differed significantly among sites, regions, and years. A distance-based multivariate multiple regression analysis revealed that the mean sediment grain size and total nitrogen, lead, nickel, chromium, and aluminum concentrations were key environmental variables determining the variation of the meiofaunal assemblages. This study can provide basic ecological data for understanding the spatiotemporal distribution of meiofauna assemblages and aid in the development of management strategies to mitigate marine pollution on the southern coast of Korea.