Compositional similarity generally decreases with increasing geographic distance between sites (distance decay of similarity, DDS). Two non-exclusive mechanisms have been proposed to explain this pattern: increasing differences in environmental conditions and pure spatial effects of dispersal limitation. On regional and global scales, environmental selection is considered the major factor for microbial assemblages, whereas pure spatial effects are generally more profound for larger organisms with limited dispersal ability. We investigated the DDS relationships at a small spatial scale (decimeters -tens of meters) for three groups of benthic organisms differing in body size: diatoms and flagellates (DF), ciliates (CL), and harpacticoids (HA). All groups demonstrated definite DDS relationships. The pure spatial effects were strongest for the smallest-size protists (DF), relatively weaker for CL and negligible for HA. In contrast, environmental factors (i.e., the differences in sediment properties) were more important for the HA and CL assemblages than for DF assemblages. In addition, we revealed a considerable temporal component of DDS relationships. First, similarity decreased with the time interval between sampling events ("temporal DDS"). Second, the average spatial similarity itself increased with time. These effects were significant for DF and CL only but were weak or undetectable for HA. Thus, our results are opposite to those commonly observed at larger (regional or global) scales. We suppose that the DDS relationships obtained at different spatial scales, despite formal similarity, reflect different phenomena driven by different mechanisms. At the geographical scale, species distribution patterns are mainly driven by long-distance dispersal processes operated at the population level and dependent on their size-related traits, which, taken in common, offer the advantage of small-sized groups. The local-scale distribution is primarily determined by individual motility and within-habitat environmental heterogeneity. Small protists are relatively less motile, finely perceived and, therefore, have higher rates of spatial decay.