We applied the elements of metacommunity structure (EMS) approach and studied the temporal dynamics of metacommunity structure in arthropod ectoparasites (fleas, gamasid mites and ixodid ticks) harboured by six small mammalian hosts sampled for three decades in the same locality in Western Siberia at three hierarchical scales (inframetacommunities, component metacommunities and a compound metacommunity). All metacommunities were positively coherent. Inframetacommunity structures varied across sampling periods in all host species. The main structural pattern in an inframetacommunity of the same host varied across sampling times but was mostly characterized by clumped species distributions (Clementsian, Gleasonian and their quasi-versions). Component metacommunities in five of the six host species were characterized by either a Clementsian or a quasi-Clementsian distribution. In four of the six host species, this pattern was driven by mite distribution. The temporal structure of compound metacommunity was characterized by a Clementsian pattern. In contrast to the majority of component metacommunities, this pattern was driven by fleas, whereas the temporal structure of gamasid mite compound metacommunities demonstrated a Gleasonian distribution. The temporal gradient in infracommunity composition was not associated with temporal changes in either air temperature or precipitation, whereas the precipitation gradient was positively correlated with the structure of component (in five host species) and compound metacommunities. In conclusion, the best-fit metacommunity structure of ectoparasites varies temporally due to temporal changes in distribution patterns that can be associated with year-to-year climatic variation, affecting both hosts and parasites.