A diatom analysis of a peat deposit from Shemya Island (Aleutian Arc, USA) is performed, and the dynamics of the diatom community are described. According to the radiocarbon dating, the formation of the deposit began 9300 cal. years BP. Principal component analysis made it possible to relate the dynamics of the diatom community to certain environmental conditions and the factors that influenced the coastal ecosystems during its formation. The following factors (predictors) were considered: the influence of age, zoo- and anthropogenic effects, and changes in climatic conditions. Sea level change was the main driver of the diatom community in the studied water body having a continuous direct and indirect influence on the studied small water body, i.e., by bird colony formation and more humid and coastal conditions. Since 3000–2000 cal. years BP, the anthropogenic factor (hunting depression of the bird colony) also became significant. During the whole water body lifetime and following peat formation, the diatom community was influenced by groups of factors: global factors (e.g., sea level rise) caused gradual change of local factors, which resulted in smooth shifts in community. In contrast, local factor influence (bird colony rise and fall due to human activity) caused abrupt and transient shifts. We can hypothesize that the relatively stable global environmental conditions in the Late Holocene were an auspicious background to see abrupt changes due to influence of the zoogenic and anthropogenic factors. We believe that further works on the material from other islands will make it possible to form a general picture of changes in the diatom communities in the Holocene and interpret it in connection with climatic changes in the region.