The present study investigated the spatiotemporal distributions of meiofauna and corresponding environmental variables in two different subtidal environments. The two habitats represent unique geographical localities; (1) Jinhae Bay for semi-enclosed industrial bay (under anthropogenic pressure) and (2) Samcheok coast for open sea area (rather in natural condition) in Korea. Biotic and abiotic data were seasonally collected from six monitoring stations in each area for 3 years (2013-16) at two study areas and all the data were comparatively analyzed. First, abiotic data such as sediment properties and water quality parameters showed significant variations in time (season/year) and space (site/area) cross the study areas and within sites in each area. Second, meiofauna assemblages, such as number of taxa, abundance, and composition, greatly varied between seasons and localities, reflecting (in)direct association(s) to local activities and/or environmental gradients. Of note, the Jinhae Bay community was directly influenced by a hypoxia during summer season. In general, the site-specific variations rather prevailed masking seasonal fluctuations, indicating significance of both oceanographic settings and terrestrial land use activities. Among the environmental parameters measured, sediment grain size appeared to be the key factor in determining the meiofaunal assemblages and distributions, particularly under natural condition shown at Samcheok. Altogether, clear separations in meiofaunal community cross sites (inner vs. outer stations) and areas (enclosed industrial bay vs. open sea) implied anthropogenic pressures and certain impacted boundaries. In addition, association of benthic communities to anthropogenic environments seemed to prevail in macrofaunal community, being simultaneously influenced by abiotic seasonal fluctuations. Overall, two contrasting nearshore habitats exhibited typical spatiotemporal distributions of subtidal benthic communities being collectively influenced by anthropogenic stresses and site-specific environmental gradients.